Generally, it should be possible to research all weapons from the start, with penalties.
I think unlocking Plasma Torpedoes and Advanced beam weapons for around 100k tech points or maybe even a Million, would be the way to go to allow players to utilize the SM functions.
An alternative would be to let the player pick a racial Strenght at start, so you could RB different races, one of them has access to most beam weapons and missiles, like now, one focuses on advanced Lasers and Microwaves, but can't use missiles without capturing them (maybe originating in a nebula?), and one has Hybrid weapons (like the PT), but lacks access to Mesons and Lasers.
Also, given the Plasma Torpedo is essentially a Short range missile that requires energy instead of ammunition, shouldn't there be also a Beam weapon that requires Ammunition instead of energy?^^