Perhaps, but 2014 is pre-#MeToo, so those risks wouldn't have been fully appreciated. SV has a long history of being able to use money to sweep sexual misconduct allegations under the rug and the current landscape of these arrangements causing PR problems for companies is a pretty recent development.
Not paying these bonuses would have certainly resulted in a court case and publicity that Google perhaps thought, at the time, would be negative. So they probably rationalized that resolving the situation by a) paying a settlement to the victim, b) ending Rubin's employment and c) not having to go to court and face that bad PR was the prudent approach.
Given how the industry (and country) has changed it's handling of sexual misconduct allegations in the last couple years, it's easy to find fault with the way they handled it, but Google's lawyers were operating in a very different context in 2014.