No, he's telling healthcare providers what they must do and not giving the Church special exceptions. Also, I've looked at the article and I can't find where he's forcing them to give birth control to their employees, only offer birth control insurance.
I've thought about this issue a lot since you brought it up, and I still don't know what I think about it. On the one hand, Obama's dictating what people have to carry, but on the other hand (besides the fact that the Pope dictated what they could not carry, which is just as bad in my opinion) that's no different than requiring smoking and non-smoking sections in resturaunts rather than allow patrons to smoke in an area where non-smokers would get offended through the smell, second-hand smoke, or taste of the food..