The only difference is that the word 'Theos' (meaning God) which comes from the Greek, is called 'theory' in science, instead of 'theology' in traditional and openly metaphysical religious tradition.
wrong. try looking up the real etymologies of the two words instead of coming up with your own invalid ideas (just because they both have "theo" does not mean they share a root).
Here's the etymology for "theory", from the Online Etymology Dictionary (quoted from www.dictionary.com:
1592, "conception, mental scheme," from L.L. theoria (Jerome), from Gk. theoria "contemplation, speculation, a looking at, things looked at," from theorein "to consider, speculate, look at," from theoros "spectator," from thea "a view" + horan "to see." Sense of "principles or methods of a science or art (rather than its practice)" is first recorded 1613. That of "an explanation based on observation and reasoning" is from 1638. The verb theorize is recorded from 1638.
1362, from O.Fr. theologie "philosophical treatment of Christian doctrine" (14c.), from L. theologia, from Gk. theologia "an account of the gods," from theologos "one discoursing on the gods," from theos "god" (see Thea) + -logos "treating of."