In leagues that use an extra category, remember that they are as valuable as any other category. Basically think about the effect that playing in a 4x4 versus a 5x5 (no SBs) has on Carl Crawford's value. So I definitely don't think you "punt" this. I mean you should use everything you can to gain any little edge. Ignoring this category for hitters is being too lazy to look for the little edge it might give you.
When trying to project hitters GIDP, instead of just using last years you should use 3 years or so to average out the ups and downs. I would bet there are pretty big swings in hitters GIDP from one year to the next. Also maybe using an average GIDP/AB number for each batter and then applying it to your 2007 projected ABs would make sure you're not giving a guy extra credit for not hitting into DPs when in actuallity they just missed half a season or something.
As far as how much to adjust them, first look at how much the GIDP swings from year to year. I imagine it's quite a bit. If this is the case then realise that while you can identify good GIDP guys and bad GIDP guys, you don't have much precision on projecting it. So I would just take the best 10% guys for GIDP and move them up slightly. However, I would take the worst GIDP monsters and move them down significantly.
Like playing with E as a category, you mostly just want to avoid drafting those hitters that absolutely kill you in that category. You should be able to do this without skewing your overall rankings that much (basically just moving 10-15 guys). So you shouldn't "hurt" your other offensive categories that much. Let the other guys ignore it and draft a couple GIDP monsters and then you'll win an extra category each week.
Oh also one more thing.... remember that since this is a negative catagory for your hitters, plugging in backup guys may not be as helpfull as it normally would. Typically these cheap backup positional players don't hit for as good of an average and/or don't produce very well in the positive stats. So you have to look at that to see if it's worth it to pick up backups to get extra games in during the week. However it's a positive category for pitchers so you may consider rotating in a few more of the lower-tier SPs to help you in W, K and GIDP (3 positive stats instead of the normal 2 for SP) versus how much they might hurt you in ERA and WHIP.