I have not made aragocrete. I have made rocks with the foam-and-silicone method.
The cement does raise your pH, but that's a good thing. Rift lake fishes love high pH. The cement will not make it too high for them. But, if you want to make sure your rocks are neutral, there are three things you can try:
1) wash rocks with acid. This is what pond and pool installers do. Stronger acids like muriatic acid work well, but are also dangerous.
2) soak the rocks in water for a few weeks, changing water frequently. Slow but sure and safe. It helps if you use water that is acidic or neutral and soft.
3) coat the rocks with clear epoxy.
You can also use low-pH cement mix (I think the article I link to suggests that) and a neutral sand, such as silica sand, rather than aragonite sand.