His philosophy was pretty weird. But in general, the theory of evolution can be incorporated into a theistic worldview. The problem I have with evolution is the science. Evolutionary theory just doesn't correspond to the available data.
The species remain, but new species arise from them. In some cases, maybe most cases, no new species arise from existing species at all; for the one case, a whole new branch could arise and flower into even more variety than the branch it came from.
This is interesting speculation, but it doesn't conform with the fossil record. The other problem is that when examined carefully this speculation falls apart. Thinking about the staggeringly complex human body, it just seems impossible that it could have developed gradually. Take the eye, for example. How could it have arisen gradually? Not only do all the parts have to be in place for it to operate, which seems impossible through chance, but all of the supporting biological systems (neurological, circulatory, etc.) must also have arisen simultaneously, which is equally implausible.