The morality paradox of religion

I can be considered as someone who isn't particularly sympathetic toward religion. Considering some of the cutting tirades I might have espoused on occasion, a not wholly unfair assessment. For anyone who sees this as an assault on a moderate "live and let live" philosophy, I feel some qualification might be necessary.
I've been turning over in my slightly troubled mind of late what I believe to be the crux of my problem with some, I hasten to add not all, religions.
A popular defence of religion as numbers of followers decline is that it promotes morality. After all, is it not the bible which taught us the ten commandments? True enough that without morality, there would be little to attract one to religion. Religion to me is essentially a repackaging of morality, presented along with examples, however fantastic, to demonstrate principles of morality. There are of course numerous examples within Christianity and I feel I should give at least one; so let's go for the "good samaritan" and it's "love thy neighbour" message.
The reverse to me though, is not true. That is to say that without religion there is no morality. One can have a sense of right and wrong without necessarily believing that there is, for example, life after death, or a "god".
So the danger for me comes when morality and religion are presented to us as a package. If one rejects those elements of religion which appear unsubstantiated, then there is a danger that one might reject morality along with it. When this happens, those who "believe" might interpret this rejection as evidence that morality needs religion. This is not to say of course that religion has everything wrong. A great many moral teachings of Christianity could be substantiated with relevant, contemporary examples, and often are by modern churches. When this approach is used with young people they then have the option of choosing a practical moral framework without needing to swallow fairy tales along with it.
I would personally go further and say that religion can, on occasion, be charged with exploiting a natural, or learned, sense of right and wrong within a potential subject to gain acceptance of ideas which are not quite so easily demonstrated. We're that to be true, is that not deceptive? Isn't there a commandment about that?....


Anyway, it's 0440 AM and now that i've gotten that out of my system, i should try and get some sleep for work in the morning!