@Deiru Right, but it is very possible that Sony set this (transferring patent rights) as a requirement to fund the game's development at all.
That doesn't mean there's no ethical implications of saying yes to that, of course, but it is very different from "Kojima patented this thing" - and given how common these sorts of clauses are, you can't necessarily assume that Kojima was aware of the *extent* of the patents that would be filed, for example.
@joepie91 Kojima is credited as the one who came up with the tech being patented.
So he at very least had part in filing them or condoning them.