[Randyman]

Here's my take:

MH, RAW, is carefully balanced at TL 8 to establish a balance between the Commando and the Warrior in terms of combat effectiveness against foes with Injury Tolerance.

The phrases italicized above are important. If you move to TL 9 or higher, the Commando's weapon suite will become more effective relative to TL 8 (issues with Ultra Tech notwithstanding), as you are discovering. Similarly, if you are using foes without some form of Injury Tolerance as MH uses it, the Warrior's weapon suite will become less effective.

Your task is to rebalance the Warrior and Commando, obviously. You can do this by diminishing the effectiveness of the Commando's weapon suite, or increasing the effectiveness of the Warrior's weapon suite. My off-the-cuff recommendations:

TL 9 weapons for the Warrior - increases the damage of the Warrior's weapons. I don't recall if the increase in Ultra Tech RAW is proportional to the increase in the Commando's weapon's damage, but you can house rule that it is.

Adjust the effects of Injury Tolerance - either to increase the damage taken from the Warrior's weapons or decrease the damage taken from the Commando's weapons. This could also be achieved by suitably humanoid foes wearing TL 9 body armor, in addition to their native Injury Tolerance. However, I do not recall how that would or would not stack by RAW.