To be honest this is sort of the point of playing a game as a commander. In real life to be a leader in the military you need to be separate, and somewhat aloof from your men, you need to be able to take care of them, but ultimately be willing to send them off to die as part of a greater plan. This is why so much effort is made to separate officers from the enlisted a lot of the time. As nice as it is to read about some heroic commander caring about their men, and respecting them as individuals, as opposed to someone who say spends their lives easily, in the real world that's not practical or expedient. Being able to send hundreds if not thousands of people to their deaths without them knowing why without becoming a complete sociopath is one of the reasons why being a commander is so hard. At the end of the day as a commander your troops are an extension of your will, your weapon so to speak, and once you start worrying too much about your weapon as opposed to winning it guarantees your going to lose, sort of like someone in personal combat who becomes so worries he might ruin the polish on his sword that he gets himself killed by taking too much care of what is ultimately a weapon that can be replaced.
Video games ultimately do a good job of showing the realities of war from a number of perspectives. In a small scale game with adventurers you of course tend to empathize with them and form strong individual opinions. When you move up to squad level such as X-com you can also empathize with your troops, but ultimately understand that any individual is ultimately disposable and realistically your going to take losses to succeed. Losing a favorite trooper can thus cause some reaction, but in well designed squad games your going to carry on after your victory and accept that loss as the price of warfare. On a grand strategy level where your moving squad, task forces, armies, and fleets, you of course have to be entirely detached from your troops as individuals.
In a game like "Homeworld" at the end of the day you have a very specific objective, while you want to preserve as many troops as possible, everyone and everything is expendable in the scope of the overall objective. Basically if you can't accept that, you don't belong in the Commander's seat.
That said there is such a thing as being a responsible commander as well, but that can't be confused with empathy, since at the end of the day as the commander your inevitably going to have to say order a bunch of people unknowingly to suicide in one area so you can say come around the back with another unit, or distract the enemy while you do something else, or simply soften up targets with less impressive units like infantry so your more valuable units like armor can carry the day.
One of the big reasons why I would never join the US military today is because I do not believe the current command is worthy of my life or service, mainly because of the way it's been unable to stand up to left wing politicians. Some people wonder at the ease of which I talk about wiping out thousands or millions of people at times as part of total war strategies, and that is in part because I believe the military has a responsibility to our own troops to fight as effectively as possible to minimize our own casualties even at terrifying cost to enemy cultures. Basically if we have a target, and a bomb that can destroy the target but will kill a thousand enemy civilians and a substantial part of their local infrastructure, I believe the military has a moral responsibility to it's own men to use that weapon. After all if you send in a bunch of troops in hummers with maybe a bit of limited capability air support to take the objective your going to lose people, people who would not die if they weren't being forced to fight gun to gun with the enemy when the option existed to win the battle with the push of a button (so to speak). Men and Women who volunteer for national service, or are drafted as a part of national responsibility (which hasn't happened in the US for a very long time) should be respected, and that means while you might have to send them off to die, you don't do so when you have any other option and other tools at your disposal. When you start putting other peoples above the lives of the people pledged to nationals service, for ANY reason, I view that as being a problem. Of course one of the other problems with American engagement policy is that our incompetent techniques are such that they inevitably lead to our own people empathizing with the enemy and the surrounding culture, and that represents a problem for warriors who should be ready to kill people and break things at a moment's notice. Empathy is for the diplomats, once the fighting starts it's a weakness. Historically speaking the most well conditioned and brutal militaries have tended to prevail, oftentimes the end of entire empires coming about when the military goes emotionally soft, and then runs into an opposing force that is as hard as steel. Sometimes being ironic when an empire carved out based on merciless military action falls because it became as soft as those it defeated, while their conquerors or destroyers are hard the way they used to be.
All of the above is of course debatable, but that's my opinion on the subject, basically if I was in the military I'd accept that I might have to die being thrown against some fortification if no other options were present. I do not accept being blown up by an IED or by some dude firing from a crowd while patrolling around in an area where such things are only occurring because some moralist decided to "humanely" try and secure the area rather than using all of our tools to render it safe even if that means killing everyone. I am not going to get my own head blown off so some politician and his pet generals can sit back in an easy chair, sipping ice tea, and making statements to the media and anti-war crowd about how nice we're being during this whole thing. I don't care if they also talk about great respect for the troops, it's not respect when you see these same things happening again and again while the military hold back, and some "leaders" even talk about wanting our troops to not carry loaded weapons at times.
In a RTS game it would be like me refusing to use artillery or actually attack the enemy base on a very easy map, and then just making firing lines of infantry, causing endless deaths on both sides while nothing is resolved and the bases on both sides endlessly perpetuate the conflict with neither side being willing (or in the case of this AI able to) to put an end to it. Sitting there as the player I could empathically proclaim "OMG, I don't want to kill the poor factory workers we can't see within those buildings, for all the soldiers running out with guns inside someone is obviously working in the mess hall and I can't kiiiill them". That by definition making me a crappy commander, and also represents an oddly accurate picture of US military politics.
