this is a nuanced subject imo because i don't think it can be a straight yes or no. i think kyle did believe he liked her, and he probably developed a crush on her eventually, but i don't think he took the time to examine WHY he had these feelings or where did they come from. because, and i dont think this should be a controversial take, nowhere did we see kyle interested in heidi BEFORE she started going out with cartman. i don't remember them having a meaningful interaction between them in all 20 seasons of south park before heiman but suddenly she becomes of interest when she gets involved with cartman.
to me, kyle saw in heidi 2 things:
1. a person he could relate to: someone who despite everything keeps showing cartman compassion and thinks he could eventually change. therefore, she was someone he could bond with. 'in a way, we're all going out with cartman...'
2. a damsel in distress, a victim waiting for her knight in shining armor and what is kyle if not a willful martyr with a hero complex? heidi was an opportunity for kyle to do what he does best: help those in need
like that, feelings started to be had in kyle's head, but not without the influence of his relationship with cartman. this is all happening in relation to the complex dynamic he holds with cartman. kyle wants to be the good to cartman's bad. he wants to help a girl whom he can simultaneously project on and become a savior of. and i'm not saying this like, kyle is a monster or whatever...i just think he's gone through a Lot and this was him trying to cope somehow.