As others have pointed out, pilates isn't a "substitute" for strength training, is IS strength training.
However, would you be likely to ask "Can I swap one of my strength training session for a session focusing wholly on my shoulders?" Wouldn't that seem odd? Substitute the word "core" for "shoulders" and that is exactly what you just asked! :)
Pilates is great core strength work. But your core is not your only body part.
Good whole-body ST should be done 2-3 times a week. If you're already doing 3, then doing Pilates only for one would be okay, because you still have 2 for the rest of the body. If you were only doing 2 and want to swap one down, I would suggest your legs, shoulders, arms are not going to get enough ST through your week for best results.
Deb, in New Zealand