Same issue, flying in & out about 10 times in the last 3 months. I ask them every time to find a page that already contains stamps and to use that page instead of a new one
yes there is no other option for you I believe unless you come from a qualifying country that allows a visa exempt to Thailand. My wife had to leave Thailand for a re-entry, and entered again on visa exempt.
You will then have to leave again Thailand to apply for the non-O visa. Unless you find a very good agent / lawyer than can do it inside the country. (We paid around 38,000 THB to my lawyer so my wife didn’t have to fly out & apply for the non-o abroad).
Make sure your wife’s employer pays for the expenses, we spend around 100,000 THB for both our 1 year visa fees including some travel expenses.