they didn't??? How come my memory tells me otherwise? Vanilla was barebones compared to the final version of BTS, and we only saw the stripped features added later in paid content, as "expansions". Granted, those "expansions" saved the game from the Shafer disaster, but still...
I believe one of the Firaxicon talks either last year or the year (or some other interview) before addressed religion in particular. When Civ5 was initially being developed, it was thought that religion might be put in the game, so some barebones work was done. But then it was quickly decided that it just wasn't going to work with the vanilla design (at least not without far more development time/resources than could be spared). Some artefacts of the barebones religion system implemented extremely early in the game's development weren't completely scrubbed out, leading some people to think that it had been deliberately stripped out to be sold in G&K - but this wasn't the case - rather, there was a very early design decision not to include religion in Civ5. Had they decided to include religion in the base game, it likely would've been a poorly implemented mess. Alternatively, they could've delayed the game by a year or two, which is about the development time that was needed to eventually get religion in the game in G&K (under a new design, by a new designer).
The practice which most people would have a problem with is putting in effort to fully create features, and then deliberately withholding them so they can be sold as DLC. The constraints on developer time which prevent every system under the sun from being implemented before the base game is released are not remotely the same; there was no option for Firaxis to release religion as a Civ5 DLC on Day 0, because they hadn't actually developed it.