You should be fine.
Stating the obvious, the fetch from any spider will still get your entire HTML code. Google, and I am sure Bing and others, will still store the entire HTML in their database. But that is where it will/should end.
Search engines use the HTML DOM object model to analyze your source code. Google, Bing, and others with the exception of Yandex, will completely ignore any keywords meta-tag found. In fact, there is no provision within the Google index for the keywords meta-tag and has not been for a very long time. That is good news. So even without the comment tags, only Yandex would even touch the keywords meta-tag.
To further your point, I have done the same thing as a quick fix to modify the HTML my site produces with positive and immediate (as much as search allows) effect. You should be fine using the comment tags to disable (lack of a better word) the keywords meta-tag. I rather suspect that even with Yandex, this will work a treat!
Not a worry. You are doing the right thing!
If and when you can remove the keywords meta-tag, I would recommend it. I know that sometimes this is not an easy thing to do. But put it on your to-do list after all the other really important items and get to it as soon as you can. Think about how nicer the holidays will be without that damned keywords meta-tag hanging over your head? The wine would be sweeter, the meal spectacular, the company a charm, the music more soothing, the night air and evening stars will be magical, and your girl will be the belle of the ball... okay, I might have gone over-board. But you get my drift.