I think indexing is the better solution than character replacement ...

index seems a very good match to your use-case.

... I don't have to think about all possible characters that could cause issue ...

That's exactly what quotemeta (and its \Q...\E avatar) does for you: escape all characters that could possibly cause an issue.

Expanding the regular expression is also extremely useful and I use it a lot in other applications but thought I had to explicitly enable it (with eval) rather than explicitly disable it somehow.

I don't understand what this means. Are we still talking about meta-quotation? Could you give an example of what you're doing with eval? (Please see Short, Self-Contained, Correct Example.)