The fountain of life doesn't know that he reincarnated. It only knows that some changes were made to Ragnarok's divine ability and that he awakened the original one. It doesn't know that Ragnarok made the changes but such a thing couldn't escape the notice of the fountain of life. But the fountain of life didn't do anything about it. The Fountain of Life chose to simply watch.
The fountain of life is a powerful entity. It is not threatened by Ragnarok despite sensing that he has a very powerful soul. Ragnarok surely has potential but potential doesn't equate to strength. Potential needs safety and time before it can become Strength. A dead genius is no different from a dead moron.
The most important reason why the fountain of life chose to abstain from killing Ragnarok for breaking the curse is that it is in a stalemate with the demon God of Carnage and it wants Ragnarok to help it. These are dire times after all.