Just get some epoxy resin. I've used the clear-coat/pour-on/etc. type that you can usually find in Lowes/Home Depot/Hardware stores in the paint/varnish section, or craft/art stores in the sculpture/casting section, or sometimes in the bigger Kmart/Wal-Mart/Target craft section.
It's a pretty easy 1:1 mix, fairly viscous. mix it up with some sand until you get the thickness you like, and use that instead of mortar/grout.
I've done this on a few paludariums, and some other odd sculpture-type things. Relatively easy, fairly forgiving (make a mistake, just coat it again), holds up fairly well, and I think it looks fairly good.
You might be able to just silicone the rocks together, and then pack the silicone with sand, but (I haven't tried this personally), I think the sand would eventually fall off and expose the silicone.
I recently ran across an epoxy-based grout in ?I think Lowes, but I don't recall the name of it, and I have no idea what it's like to use, I think it had some ASTM rating or something. Might be worth looking into.