When Lenny took the job of directing TSFS, he has been very clear about the fact that The Studio would not get off his ass the entire shoot. Even getting to direct this movie, which seems so obvious and logical to do, was almost reluctantly given to him with the reasoning - or the excuse - that his book stated how he really hated STAR TREK in general and Spock, in particular. None of it true, of course. This was cleared up through subsequent discussion, but there was a lot of lost time, as a result. And it may have even had to do with the fact that Nimoy had the brass balls to sue Paramount in the first place for use of his image, prior to TMP.
So, on top of all of that political nonsense, once he finally did get the job of directing, he's immediately handed the problem of Kirstie not reprising the role. Leonard simply went the path of least resistance and I don't blame him for it, at all. He practically invented the Vulcans, through Spock, so he followed his strengths. He emphasized Saavik's Vulcan attributes, which he understood extremely well and solved this problem that way. Kirstie Alley put her stamp all over the Saavik character, without her, Saavik was going to be dramatically different whichever way it went. Nimoy was right to handle it the way he did, with all of the pressure he was under.