I haven't read the comics in question, but her taking over the science office position doesn't make much sense to me. She has command school training, and was at navigation during TWoK; what qualifies her to serve as science officer?
Don't forget Decker took over as both exec and science officer
in TMP before Spock rendezvoused with the ship, because he was, apparently, the only qualified individual in the entire crew! I realize that the Enterprise was just getting ready to launch, and not all the crew was aboard, but really, there were only two people on the entire ship qualified to run the science station?
So I guess Saavik would've been qualified to run the sciences station in STII.