Intuitively, I choose "meta-mer-ism" (or, rather, "me-ta'mer-ism"), probably for the same reasons you choose it.
But English isn't an intuitive language, and various English dialects pronounce things differently.
Just listen to Michael, a New Yorker and a BBC reporter when they say the word "about", for instance. The intonation and rhythm is quite different.
I'd love to see what the OED had to say on the subject, since it tends to be a very good descriptive dictionary.
Here are some other opinions on the pronunciation:answers.comdict.die.networdwebonline.com
The former two seem to mostly agree with our intuitions, the latter with M-W and Canadians.
(Oh well, I guess you would have had to have seen the movie ...)