Buying endorsements probably isn't the way to handle them, but it would take a very serious change to make it any other way.
Would getting NOW's endorsement really hurt Bush among conservatives? Would they really then vote for the liberal party to just spite a conservative reaching out to different groups? No, they probably wouldn't. They might not vote for Bush in great numbers, but in Pol Machine turnout is measured by awareness and awareness is a statewide trait (ie. its not different for Dems, Ind, and GOP voters). So you can't possibly be arguing that getting NOW's endorsement should reduce Bush's awareness?
The penalty for getting this pro-choice endorsement is very minor. Having your abortion position shifted a little bit isn't usually going to cost you many voters, unless abortion happens to be a top 3 issue somewhere. That is probably the major problem. The AI uses endorsements as free national awareness boosts and often takes just whatever ones he can get, without caring about how it costs him in terms of issues. I've seen someone get both the CC and NOW. I've seen them get the Chamber of Business and Unions. Actually, I sometimes have let the AI get all but one or two of the endorsement groups because I needed spin doctors and smear doctors in key states, more than I needed a slight boost to my awareness in Montana.
I'd like to see endorsements reworked, but unless you just make them endorse candidates who advertise for their issues or make them cost a ton if you don't agree with their positions, I'm not sure what can be done.