Firstly, Kojima wasn't ever supervising anything on any of the LoS. They merely encouraged and lent technical support.
Secondly, thats reverse logic there. If the game flopped hard enough, they wouldn't be allowed to do another sequel, which is the opposite of Konami asking them to make up for it by making another sequel. They would be 'free' to pursue their dream game cause they'd likely not get another contract with Konami. LoS1's success may be still keeping them afloat here potentially, but we wont ever know.
You don't necessarily get the go ahead to do your dream project by pleasing a publisher. You usually do what the publisher wants you to do. Publishers want to do what will make the most money, which means follow on successful leads. LoS2 might not have failed to reach it's mark afterall, or LoS1's success made up for it a little, and they convinced Konami they'll do another like LoS1 again.