There really isnt much of a balance issue between IS and Clan if true cost (BV or C-Bills) is taken into account. Sure he can afford a Mad Dog but for the same coin the IS could field a Catapult and a bunch of tanks.
In NBT-HC a MW4 Mercs "puretech" league (Clanners had Clan weapons and vice versa). Even without a BV or C-Bill system in place for non-league no-respawn puretech games the bias was 50/50 Clan/IS why?
An Avatar (IS 75ton, fast) with 2 RACs and a couple of RL15s with 16seconds of ammo, ECM and max Reactive armour could hand any 'mech in the game their hides on a plate fast. Blood Asp or Atlas, you fall fast to that monster, only the fast movers stand a chance. And sure your PPCs lose 100m on theirs, and a Warhawk carries 4 to your 3, but you can field 2 Awesomes (or thereabouts, like 2 Shrecks and a Medium 'mech I think) for the price of a Warhawk (so that Clanner pilot better be good). Regardless its purely illustrative, the point I'm making is the the same.
If the Clanners have to pay more for their greater firepower capacity, and even their greater range (liked my old IS weapons with their faster recyc times and whats a 100m or so between friends?) if the Devs implement Clan and IS weapons I'll be happy standing with cheaper kit and numbers on our side. As the Clanners would say "Imagine the glory we'll gain by besting them with inferior equipment, quineg?".
Ultimately, I don't see puretech as much of a problen as long as costs are balanced. As it stands the Clanners already have a significant advantage (and rightly so they're more advanced) in that their chassis have more weapons tonnage (compare the Blood Asp load-out with the Awesome, you'll find that IS Assaults compare in firepower to Clan Heavies and Clan Assaults have no counter!! This is even more obvious at the bottom of the food chain....the Adder(Clan, Light 'mech) can carry the same long range support firepower as a Catapult (IS, Heavy 'mech).
But I think this, if its implimented would be a build away.....