"in someone's eyes" meaning "in someone's opinion" (AE) and punctuation with phrases of opinion
Solution 1:
As you've shown, it's the comma placement that matters:
A. Sulfuric acid, in my eyes, is useful for unclogging sinks. (okay)
B. Sulfuric acid in my eyes is useful for unclogging sinks. (ouch)
Edit: Placement of the idiom is also helpful for reducing ambiguity:
A. Pointy sticks, in my eyes, are great for roasting marshmallows. (still problematic)
B. Pointy sticks are great for roasting marshmallows, in my eyes. (better)
Edit edit: I do like it better at the beginning of a sentence, but it doesn't always work:
A. In my eyes, Sulfuric acid is useful for unclogging sinks. (better)
B. In my eyes, tiny aliens exist. (still ambiguous)
There are instances where it might be better to just use "in my opinion" instead.