hmm, if I think of a more realistic way of limiting the retraining of units, it would be the size of the population of the city (or, at least, the settlement's).
e.g. you can only train/retrain 1 man per 100 population in your city.
or you can only train x men for small town, 1.5x for large town, 2x for ... etc.
You get my point.

About the units gaining bonuses from foreign cultures' temples: well, it may seem a bit odd, I agree, but would you rather have them get no bonuses whatsoever until you build your own temples in that city ? I suppose one can think of them in a similar manner that one gets the upgrades - it's just another type of upgrade, and they stack.
(like in MTW, you could retrain a gold armor unit in a province with gold weapons only, and it would keep both bonuses).
I agree however that it would be definitely weird if they actually _kept_ that bonus, and stacked the bonus from Roman (or whatever your faction is) temples.
i.e., they get +2 to missile attacks from Abnoba, but they also get whatever other bonuses your own temples offer when you retrain those units in a city with that kind of temples.
This should be tested