I'm not religious at all but even so, a church, temple, synagogue, or mosque being part of the building wouldn't phase me either way. It could sway those belonging to the denomination to maybe buy a unit to be close, but at the end of the day I don't really see the big deal.
I actually think it's great to incorporate the church because quite frankly most of the places of religious worship out in the suburbs so inefficiently use the land and waste space with a lot of surface parking. To have a church be represented in city center for those that call it their place of worship and at the same time be part of a dense "downtown" development not wasting space, is something we should do more of out here in the burbs.
Mixed use right? I'd call this a light mixed use project. Retail, church, and residences all in 1 place.
That said I would be surprised if the residents are sharing a parking lot just like in Park Place the residents aren't sharing a parking lot with the rental/commercial parking spaces. They have their spaces then there is a giant gate to protect the residential part. If you mean though that the project is losing out on residential parking spaces in favor for church/retail parking, then you're probably right. But it is a downtown style development and most Vancouver towers going up have less than 1 parking space per unit especially developments practically on top of SkyTrain like this one.