At the very end of this 2006 interview (rm), Kontsevich says

"...many great theorems are originally proven but I think the proofs are not, kind of, "morally right." There should be better proofs...I think the Index Theorem by Atiyah and Singer...its original proof, I think it's ugly in a sense and up to now, we don't have "the right proof." Or Deligne's proof of the Weil conjectures, it's a morally wrong proof. There are three proofs now, but still not the right one."

I'm trying to understand what Kontsevich means by a proof not being "morally right." I've read this article by Eugenia Cheng on morality in the context of mathematics, but I'm not completely clear on what it means with respect to an explicit example. The general idea seems to be that a "moral proof" would be one that is well-motivated by the theory and in which each step is justified by a guiding principle, as opposed to an "immoral" one that is mathematically correct but relatively ad hoc.

To narrow the scope of this question and (hopefully) make it easier to understand for myself, I would like to focus on the second part of the comment. Why would Kontsevich says that Deligne's proof is not "morally right"? More importantly, what would a "moral proof" of the Weil Conjectures entail?

Would a morally proof have to use motivic ideas, like Grothendieck hoped for in his attempts at proving the Weil Conjectures? Have there been any attempts at "moralizing" Deligne's proof? How do do the other proofs of the Weil Conjectures measure up with respect to mathematical morality?