My daughter got married at The Sanctuary which is on Exposition & Windsor, about 5 mins. from downtown. It used to be called Tarrytown Baptist Church many years ago. I think it seats about 200, but we had just a little over 100 and it didn't look too empty (see pic). Their web address is http://www.sanctuaryaustin.com/. Their wedding coordinator, Susan, is very friendly and easy to work with. The church is VERY accommodating in terms of decor, etc.
I grew up at university Christian church at 21st & university. Sanctuary is really pretty and it is right across the street from the south mall and ut tower. I am getting married there on oct 9th! Hope you find something you like!