Node comments field are a bit too big.

This is a finnicky one. Large comments are nice for clarity for short labels on things, but longer comments, like you say, just aren't viable.
A global scale can cause issues with comments overlapping for some people, and others not, depending on their current scale. Ideally, the shaders or at least the comment size should be consistent.

So there are two ways of solving it as I currently see it:
1. Auto-scale based on string length
2. Allow the user to toggle between a large/small comment

I think I would prefer #1!

Could also have a small comment icon representing a comment is present and clicking on it reveals the comment.

Possibly yeah. Mouseover to show full version perhaps?

Why not let the user set the comment font size?

I care less about font size than the ability to have multiple lines in my comment. Having it restricted to one line really limits me to a short phrase at best. (I tried /n, but it won't let me do that)