Ah, this reminds me of the times where I was on Study Island. Playing a lame, cheesy flash game where you either had to get your ladybug across the street to a particular answer, or shooting down an answer in a Space Invader rip-off... but still, it was pretty fun. (Even though I can't remember much of what I learned from it, seeing as how I haven't had to use a derivative or algebraic functions for the three years I have never had to use them.)
Now, as for my views on this issue, it's going to be the same as what everyone else has been saying, "If they're learning, so what?" and any game that allows you to shoot stuff is going to be condemned by any ignorant parent or politician before they even get a chance to play it. "GAYMZ WIT GUNZ R BAD, DEY RAYZ R KIDZ 2 B HOMEYSYDAL MAYNEEAKS!!" Says the masses, but hey, if kids can learn how to shoot straight AND get straight As on their report cards, I think you have a mommy-and-daddy pleaser and the masses should probably shut their goddamned mouths. Violence is a part of everyday life, and raising your kids in a "puffy clouds and lollipop" environment is going to make your kids extremely disappointed whenever daddy comes home one night, smelling like a brewery and a strip club, and beats the hell out of mommy and then the kid realizes that nothing is going his way and life's not fair and so on.