The Ra’av (Bartenura) indicates that one only receives reward for refraining from a lav which tempted him. (Makos 3:15)
It seems that motivation does matter.
Certainly, he won’t get punished for being mechallel Shabbos, but neither will he get schar (and even if he does, as the poshut pshat in the Mishna seems, it wouldn’t be as much as for someone whose motivation was purer).