Just because something is 2000 years old doesn't make it right.
Doesn't make it wrong, either. The age of an idea is irrelevant to whether it is correct or not. (And in religious debates, whether an idea is "correct" or not is often either impossible to prove or entirely irrelevant... at least, that's true if your goal is something other than hurling insults.)
But where I do have a problem is when the members of the church try to deprive the rights of homosexuals outside of church.
The fundamental problem with arguments about gays and/or homosexuality in general is simple: nobody bothers to agree on terminology up front. If terminology were agreed on before a debate were started, then the nature of these debates would be quite different. This is the mistake you are making.
Suppose I create a club whose only requirement for membership is that every club member must wear a red shirt at all times. Now suppose I tell a club member that I will kick him out if he continues to wear blue shirts. Would you embark on a campaign to get the Red Shirt Club to change its rules so that the member who wants to wear blue shirts can feel included?
Now suppose I create a chain of nonprofit clothing stores using my club's logo, and the store only sells red shirts and red-shirt-related items. How would you respond to salaried store employees who complain that the requirement that they wear red shirts at all times, even off the clock, stifles their freedom of expression?
Suppose I set up a club-funded hospital, and open it to everyone, but only provide red hospital gowns. What would you say if a Blue Shirt Club member comes in for treatment, then later refers to the doctors' unwillingness to provide a blue hospital gown as persecution or intolerance?
Suppose I fund an adoption agency, under the restriction that the adoption agency can only place children in homes where only red shirts are worn (whether or not the prospective family is part of the club). What would you say when a Blue Shirt Club member complains that the Red Shirt Adoption Agency denies their adoption application?
My point is, it's not relevant whether the club's rules are frivolous or even plain stupid. It's not even relevant whether they're right or wrong. What's relevant is that these are the rules applied to club members and people who want certain types of service from club members. Is it really reasonable to force that club to change its fundamental rules in the name of being "open-minded" or "accepting" or "tolerant" or whatever?
It's a waste of time to tell red shirt club members that they're being bigoted or whatever for not allowing blue shirts in their club -- and it misses the point entirely. Furthermore, none of the above scenarios require that the Red Shirt Club members believe themselves superior to anyone else in any way, and it's a mistake to assume otherwise.
In this situation, if you want to argue about something, argue about whether the behavior in question is itself acceptable, not about whether it's acceptable for the group to deny membership to people who engage in it. Of course, at that point you leave the realm of what can be proven as fact and enter the realm of doctrine... That's probably why most non-religious people simply don't try, instead accusing Catholics of bigotry or being anti-gay or whatever, without actually trying to understand what Catholics believe and, more importantly, why.
Personally I don't see why it's a problem for a group that believes a particular behavior is a sin to ask its members to not engage in that behavior, or to prohibit hospitals it funds from providing services it finds morally objectionable, or to go around trying to convince everyone else to share those opinions.