Agree with Kevin_K.
Depends on the level and how the catcher receives the pitch. Younger kids, I'm trying to grab every strike I can, but even then, there are limits. Unless that pitch is right over the plate and the ball drops right in front of the catcher, It's hard to call a strike on a pitch that a catcher butchers. If that ball rolls a few feet away with the catchers glove moving out of the zone while he's trying to grab it, that's not a pitch that you can usually call for a strike.
Almost every time I've balled a borderline pitch that the catcher butchers at the HS level, if I hear anything at all, it's usually from the coach telling his catcher something along the lines of "you cost your pitcher a strike" or "you got to hang on to those."
At the higher levels, it's almost expected to ball a pitch the catcher doesn't handle properly. There are times that you can call it for strike, and times you shouldn't. Experience and the level you're doing can help guide the decision.