While we may be committed to the spread of secular thinking and possibly atheism, we should structure our reasoning for that separately from our concerns for liberal social values. There are pragmatic reasons for doing so (enabling solidarity with liberal religious, etc etc), but there are more important philosophical reasons. The majority of the practical content of a religion is its life philosophy - we may consider life philosophies as a whole to be a wide sphere of possibilities, and religious life philosophies versus secular ones as being a simple division leaving plenty of possibility on both sides. We have a life-philosophy (as individuals) and are in the process of constructing institutions and a shared space out of our individual intuitions. Are religious life philosophies inherently harmful? I claim that our primary contention with them is that they are based on factually wrong premeses/truth-claims, e.g. that there are gods, there is a soul, there is an afterlife, there were prophets, etc. If we want to build systems to replace them, our particular problem with them is to have systems without these elements. If we want to build new systems in general and must defeat the old to allow our values to triumph, that is a separate reason and we should not confuse them (we could very well imagine creating new religious systems with whatever value commitments we desire).
If we were to imagine, for example, an alternate history where Christianity, Islam, and Judaism were moral philosophies with no claims to transcendence, that provided traditions, ways of looking at the world, judging actions, etc, we could do so, and we could in fact imagine all the events of history happening much as they actually did. A secular Christianity might still have oppressed all other life philosophies during its spread throughout Europe, might still send missionaries to spread its grasp, and might still perform all its charities and half-charity-half-evangelism tasks. Likewise with Islam, likewise with Judaism. They might still include or exclude in the same ways, might press their values as strongly. Would we find this less objectionable? To me, the answer is at most "a bit", purely because of those factual claims. The discomfort most seculars feel around the religious is exclusion from the community and life-philosophy, combined with the fact that our own value intuitions lead us to different conclusions than those of the religious. The first is in fact unavoidable - any value philosophy with content will have borders and will "want" to spread. The second is a simple pressure for us to make something new that better matches our values rather than a set of values created by people varying numbers of thousands of years ago.
A careful understanding of these factors will help us deflate naïve criticism (e.g. new atheists who would drag their heels at the creation of any new value system on grounds that it makes us "just like the religious" they left to be free of) and have reasonable expectations and goals for what we would build.