I've had the same issue before, and it was frustrating! I ended up switching to larger isopods that my gecko wasn’t as interested in eating. If you're looking for a good source, postpods.co.uk has a nice variety, including some that are less appealing as a snack but still great for cleanup. Sometimes, adding more hiding spots for the isopods helps too, so they have places to escape when needed.
I have diary cow isopods in my enclosures which are anywhere from 1/4" to nearly 1/2". Sometimes I wish the geckos would eat some because they really proliferate!