Doing a weight check on the way in will potentially hold up the whole group. If everybody else is waiting at the bottom of the mooring burning through their air, you won't be very popular on the boat.
My plan would be to overweight on the first dive and do the check between dives once the boat is moored at the second site or sort out the issue before hand. If you try to do a buoyancy check at the end of a dive you will have an empty, buoyant tank so not the solution.
I have never heard the notion that a weight check with an empty tank is a bad idea, in fact it is the most accurate way to do it.