which I linked to on Hirhurim a slight while back, and suggested a reading of the gemara.
Another two possibilities to consider:
1) Abaye mentioned lice eggs. One need not answer, as did the setama digmara, that this was another species called "lice eggs." Indeed, some species can reproduce via parthenogenesis yet still laying eggs - that is, they lay the fertile eggs without first engaging in peru urevu. Thus, a pasuk that refers to lice eggs, or a brayta that refers to lice eggs, not not imply that lice are "fruitful and multiply," that is, engage in sexual reproduction.
A case in point is the soil mite, which does exactly this -- lays eggs but this reproduction is asexual.
2) A second possibility is nishtaneh hatevah, such that if back then the assumption was asexual reproduction (well, it seems that the setama denies that lice eggs exist at all, and must therefore assume spontaneous generation, likely from sweat, with the lice eggs as living creatures perhaps coming from the lice or not, as Rabbi Slifkin suggested). But still, we can appeal somewhat to nishtaneh hateva, with once again the soil mite as an example. It used to reproduce asexually, but has just evolved once again to a state of sexual reproduction! This might also account for the machloket between Rav Yosef and Abaye - perhaps there was a similar shift in one direction or the other back then as well.
And of course there are the other suggestions, previously mentioned.