It's hard to tell from the images what it actually sounds like, as there's no time-scale, but that's the criterion I'd use - *what it sounds like*.

If you can very clearly hear the timing difference; if it sounds 'poor', then by all means shift & stretch one until it doesn't. Small time-stretches will not be heard anyway, assuming your DAW has a decent algorithm to do it. 

A good way to do this type of edit is cut early, before the next transient [always cut at zero-crossings anyway, but cutting early helps this too].  
You can then slide your transient into place, time-stretch then apply a short cross-fade to the part before it.  
Cutting early means you don't hit the transient with your cross-fade, it's done in the tail of the preceding note, so you'll never hear it.

What you **don't** want to do is end up actually quantising both so hard that all aspects of feel disappear & you have a perfect but completely sterile guitar part.

There's a lot to be said for interplay between almost identical parts spread left & right. If you sterilise them completely, the 'magic' will disappear.