My church does not recognize the JWs as Christians, therefore the reason for my baptism (not a re-baptism). I didn't have any problem with that whatsoever.
Every religion has "rules." Every cohesive entity has rules. There are rules at work (if you're absent too many times you can be fired. You cannot sexually harass anyone... etc. etc. etc.) There are even rules here (posting limits, etc.) Rules for living in the good ol' USA (pay your taxes or go to jail!)
I didn't find it unreasonable to be asked to be baptized a Christian at my church. It seems to be the only rule I've encountered so far, except for the request to keep my cell phone turned off during the service! LOL And both rules make sense.
And the difference is... no one in my church would have "shunned" me had I continued to attend and not be baptized. I'd get some pretty dirty looks though if my cell phone rang... :)
Hugs 2 U
PurpleV