I am having a new A/C system installed. The old one (condensor/compressor) was 240v 3 phase. Can the new one (240v single phase) be wired using 2 hot for single 240v?

Yes but make sure you can obtain real 240 single phase. Many three phase systems use a stinger leg and other methods to make three phase power that might no be compatible for use for a strait single phase unit. You might check with the utility and you may also see what pulling two legs off three phase power supply will do to your demand meter if you have one.It is real simple to change single phase to three phase because all you have to do is buy a rotary phase generator set up.