I believe a willingness to investigate this thorny issue of religion vs. philosophy is vital to the future of Buddhism. This religion/philosophy dichotomy which we take for granted is a relatively recent invention of the West. The separation between the two really only developed in about the 16th or 17th century. It is this separation between religion and philosophy that allowed for reason and rational (scientific) thought to reign supreme. The religion/philosophy dichotomy also ushered in secularism. And it is through the filters of this religion/philosophy dichotomy that the West discovered a 'universalist', 'rationlistic', and 'pragamtic' Buddhism in the around 19th century. Needless to say, such an understanding of Buddhism persists today.
So, it seems to me that we contemporary Buddhists are in an interesting position to see how our understanding of Buddhism is made possible by a certain development (i.e. the separation of religion/philosophy) that didn't exist in both the Buddha's culture and other Asian cultures where the dhamma took root. This doesn't mean that it is 'wrong' to read the dhamma through a rationalistic or 'scientific' viewpoint. Rational inquiry is important and it has certainly helped us understand the dhamma in new ways. But given how such a viewpoint is not absolute but conditioned (conditioned but not without merit), then, I think it behooves us to reflect carefully one how we approach the dhamma so that we do not pigeonhole it in some category or the other, and hence, foreclose its possibilities.
To give an example: I'm sure we’ve all encountered debates where people try to argue for the absolute certainty of certain doctrines. These people might hold the conviction that doctrines like dependent origination, karma, rebirth, etc, are true/false propositions and that there is no other way to accept such doctrines except on the basis of 'yes' or 'no'. But such an approach to Buddhism has its limits, shaped as it is by post-Enlightenment Western philosophical concerns with the centrality of rationality on all matters, and failing as it does to account for the richer, more complex and 'aesthetic' ways in which humans experience and express life. I don't know about others but I'm unable to express the profound effects that Buddhism has had on me solely in rational terms. There is for me a whole affective or emotional dimension that is beyond rational explanation but equally powerful and valid. I think we could do worse than prevent this dimension of Buddhism to express itself. And one way of doing this is, I think, is too let go of this religion/philosophy dichotomy.