I usually go for the side of TT and lore in most cases, as I want this to remain a BattleTech game (like it says in the title now for MWO). However, many of the people in this thread arguing against the OP's point, seem to have forgotten that PGI has already diverged from TT and lore in a major way. They have already stated that they want the Clans to be EQUAL to the IS. PGI's current intent is that if you take a 70 ton Clan mech against an IS 70 tonner, you have NO clear edge or advantage in regards to technology. They want matches to be 12 versus 12, with the Clan 12 not being able to blow away the IS 12 due to having the superior weapons and mechs. The numerous nerfs to Clan weapons aren't accidents, they are intentional changes to balance out a game where IS mechs fight against an equal number of Clan mechs.
In the TT the Clans usually operated at a numerical disadvantage for their superiority in firepower and survivability. They also orginally had to operate under strict rules of engagement, such as engaging targets seperately in duels and never combining fire on targets (unless the enemy broke those rules first). Under the typical Clan rules of engagement, you would never see the widespread use of 'indirect' LRM fire that happens so often in a typical match. However, PGI has decided that implementating those limits would be either impossible or undesirable, and instead have gone with a model of limiting Clan tech to make both sides equivalent.
As long as PGI continues to run with that model of 1 Clan mech = 1 IS mech, I see no problem with removing the insta-death rule for IS XL's, to bring the game closer to actual parity between the forces. As far as STD engines becoming extinct, give them some other bonus (such as increasing the number of internal heat sinks they can carry over XL engines). Though PGI has already made STD heat sinks extinct, subject to a 1.5 million C-bill tax for their removal, so I'm not sure how it would even matter except as another C-bill sink to buy the new engine.
And if this somehow gives IS forces a sudden edge over their Clan counterparts, then maybe PGI could loosen certain restrictions on Clan tech and customization, like removing fixed equipment/JJ's, lowering heat or beam duration, maybe even changes to Clan AC's like shorter bursts or even single shot versions.
PGI has already diverged from TT/lore, which to me sucks, but unless they reverse THAT decision sticking to each dotted I and crossed T of TT rules is pointless, the ship has sailed (and hopefully isn't the Titanic
).