I chose rewrite. I ummed and ahhed over this, the correct choice is to ask the heretics which they would prefer, but thats not possible because of the war.
The way I see it, rewriting changes one choice someone made, death changes every choice someone made. Including the one that we rewrite. They chose to serve the Reapers? Well I don't think they can do that dead. Death destroys every dream they had, every hope, every plan, every aspiration. Whatever they wanted to do the next day, is going to be rewritten for them.
There are decisions that people view worth dying over, lots of religious people would rather die than have their faith forcibly taken from them, and history is littered with examples of this. Other people have taken death and torture for their ideals, country or fellow human beings.
But the point is, since we can't talk to the Geth, we can't find out if this is one of those choices. If someone killed me because they assumed I'd rather die than have my dislike of coffee rewritten, I'd be pretty pissed off (and dead). Maybe this was important to them, they left the Geth over it, but they're machines, we don't know if that was just because it was natural for any incompatibility in thought to separate itself out. Maybe it was important to them, but wasn't as important as their dream of becoming a truly unified consciousness or whatever and killing them would prevent that. Better safe than sorry.(incidentally, total BS in ME3 isn't the effect of this choice, but that the heretics split with the Geth specifically because the Geth believed that using Reaper tech(or any alien tech) to become unified was wrong as it limited their ability to self-determinate as a species.)