well, at least none of the schools are awful, so that's a start. I too would be worred about the large state school's somewhat anti SN culture rubbing off on ds2 and3.
FYI, once ds2 is 5 years old, you should have lots of holiday club and afterschool club options opening up. That's assuming your area is like ours. 5 is the magic age! Don't get too hung up on choosing a private school because they offer after school and holiday playclubs.
Our council runs lots of clubs for children (as do private organisations), they are reasonabluy priced and you don't have to attend any particular school to go to them. However, it's worth checking what after school clubs do school pick ups from your prospective school. If the club is near the school, and several children to go it, a school pick up is more likely. If the after school club is not attended by anyone else from the school, you may have to make your own arrangements in getting ds2 to the club. I have to do this with my ds2 - another mother picks him up after school and drops him at his afterschool club. A hassle to arrange, but not impossible!
To me your choices seem to be the church school (apply and see what happens whatever the case), the private school or another state primary school if there is one.
Think also, if you go for one school, and it doesn't work out, how disruptive would it be to move to another one? ie would it be worse moving from church to private or from private to church?
If you decide to pay the fees, what the private school offers in terms of education and flexibility, will it counterbalance the possible stress of you being poorer, and how would this impact on ds1 and you?
regarding the church school, why are you sure that ds3 would find it hard to get in if goes? is the criteria just church commitment and nearness to the school? does having a sibling at the school not count for anything?
can't think of anything else at the moment, but will come back if I do!