Maybe.

1. During the period where she either miscarried or aborted, Kay was under virtual house arrest under Tom Hagan’s supervision. Tom was ferociously loyal to Michael and would never have permitted Kay to go out for such an errand, nor given the necessary parameters would she have been likely to slip it past him (see point 2).
2. Abortion was illegal in Nevada in 1958-59, without exceptions. It would have taken a substantial bribe either to a street lady or an even more substantial one to a licensed medical practitioner in a very discrete location to make one happen.
3. It’s not clear how much time passes between Michael’s return from the a East Coast and Cuba and his subpoena in D.C., but if Kay had actually aborted intending to leave Michael, wouldn’t it have made more sense for her to leave as soon as he got back? (Unless of course she feared physical restraint - not unreasonable given the house arrest - and D.C. was her first “window of flight.”)
4. Murdering one’s own child to blunt and escape a cold-blooded Machiavellian tyrant is pretty cold-blooded and Machiavellian in its own right. Merely saying that it had happened seems to be a good tactic to provoke a schism, which it did, but I don’t think Kay is anywhere near as cold-heartedly Machiavellian as Michael and even he wouldn’t directly murder one of his own children on such grounds.
5. Further to point 4. her tone and demeanor when she tells the tale ring false, a hint that not only is she lying but also that she’s a less Machiavellian person than Michael and a less convincing liar.
6. I’ve not read any of the books, but I’m told that in one of them Michael had the family doctor killed believing it was he who had performed the abortion and Kay, horrified, confessed remorsefully that she had in fact miscarried but she had feigned having an abortion to hurt Michael. I realize the books are not film-canon and I also understand Kay evolves somewhat differently in the novels versus the films but given the close collaboration between Puzo and Coppola plus the above evidence this has to be at least a hint as to the narrative intention.