No it is not. An assertion by any measure is weaker term than an affirmation. In the context of the professor statement, "If you cannot truthfully and forthrightly affirm", it is a much firmer statement that simply to affirm, and in context it is most certainly more like an oath than an assertion.
Well, let's see: Dictionary dot com says,
af·firm v. af·firmed, af·firm·ing, af·firms v. tr.
1. To declare positively or firmly; maintain to be true.
2. To support or uphold the validity of; confirm.
So no, it only means to positively or firmly maintain to be true.
So he just said you can't tell me a scientific origin of humanity that you maintain to be true, then you don't get my reccommendation.
As is his right.
It would also be within his rights to refuse to give letters of personal reccommendation to someone who wasn't against abortion, if he so chose.
Cuz it's a personal letter.