This answer would not be the way it is without the other answers. They each deserve an upvote! I have unfortunately run out of votes (DVL12).
Could you be
CONSCIENCE?
My prefix is against it all
CON (thanks to @Cashbee).
My infix SEEs my EYE, did you hear what I did there?
CI (thanks to @jc1850).${}^1$ The word conscience also refers to the third eye, and there is a saying "see no evil, hear no evil (and speak no evil)".
${}^1$SEE + EYE = C + I = CI.
My suffix waited a long time, but did not mind
SCIENCE. Science can take ages (simply put, from experimenting to rock formations). Also, the word mind has to do with conscience, the latter word sounding quite like PATIENCE (thanks to @Cashbee, again).