For we have an accepted principle from the ancient rabbis, may their memories be blessed, that no objection raised in the Gemora [against an authority's position] totally disproves [that position]. It is only an objection [strong enough to discredit the theory] in the eyes of the opponents raising it. (Chiddushay HaRamban p.2 on Bava Bassra 2b cited on page 15 of Dynamics of Dispute by Rabbi Zvi Lampel, JudaicaWhile the Gemara cites an alternative to Abaye's evidence for the reproduction of kinim, it can not be said that it demonstrated conclusively that Abaye was incorrect in arguing that kinim reproduce. Similarly, and I believe relevant not only to this question but the general approach of the previous post:
It may strike some as very counter-intuitive to argue that R. Eliezer wasn't describing abiogenesis but I believe that is because most not only have a basic familiarity with modern biology but in the process where taught about the theories it supplanted. Indeed I would suggest most of us may have as much or more familiarity about the theory of abiogenesis, of spontaneous generation, that most layman did when it was accepted by the naturalists. Our cognizance about these issues is not the result of personal intellectual curiosity but of the aggressive education we have received in the modern era. While there where certainly those who did, it is a bit anachronistic to expect that when the average spoke of "sunrise" it implied to them that the sun rotated around the earth when viewed from outside the solar system. Likewise I think it is a bit to much to infer a reproductive theory from Chazal's description of things from the standpoint of a human observer. As such I think it it is prudent to be very caution about reading too much into their words especially when it leads to attributing error to those about whom it is said "nevuah was taken from the Nevi'im and given to the Chachamim" (Bava Basra 12a).
For everyone who studies our Talmud knows that when our commentators disagree over something, no one of them has any absolute proofs for his side, now matter how many difficulties he can raise against his opponent. Our subject is not simple mathematics, in which only one conclusion can possibly be reached. In every talmudic dispute, all our strength and might is devoted to laying aside one opinion in preference to another by means of logical evidence. We then interpret all [related] statements in that light, sometimes in a forced way. We give the seal of approval to the total picture which seems easiest to accept, considering all the data involved. This is our goal and the goal of every G-d-fearing scholar of talmudic science. (Ramban, Introduction to Sefer Milchomos Hashem, cited ibid page 16, emphasis added)