Is it worth losing ~200-250 tower attack to hit 90/90/90/90 or 50 on NM resists?

As a tower char, all you do is swap him in, set some towers, swap out for dps.

I mean for nightmare, where you'll probably need your apprentice to be in during the wave for combat repairs + quick setup of new towers

Just repair with the dps char. :]

repair is fast with any hero now, but I use my app for DPS to get that 33% bonus from towers, and to rebuild if towers go down. Thats the only reason you would want resists up. the 33% bonus makes up for the lost points.