He was a human being with flaws and bad habits. But a rapist? Sorry, not without proof.
One thing Grace Lee's claim reminded me of was Nichelle Nichols charge that she too had been sexually harrassed - in her case it was by a low-mid level NBC studio executive (others here may have a sharper recollection of the details). So, sadly, sexual harrassment was/is a part of the Hollywood landscape, but I don't think Roddenberry ever "forced" himself on anyone. In a screwy way he was one of the "good ones" who actually followed.
Also, for my own peace-of-mind, I just want to say I still think Gene Roddenberry is deserving of a lot of credit for a lot of things. I believe, upon reflection, that part of my negative feelings toward Gene Roddenberry actually may stem from Rick Berman's overplaying the Roddenberry card in stiffling and strangling "Star Trek" - but that is a discussion for another thread.