For MA Strikes, using the LA or SL tables make sense, at least as much sense it does for other weapons. A dagger crit does the same damage as a two-handed sword crit on the same roll. Unless you remake the table for all weapons or classes of weapons versus LA and SL I don't see a problem with MA Strikes using the same table.
For MA Sweeps we did things a bit differently. We allowed MA Sweeps against humanoid opponents (determined by GM), otherwise MA Strikes was the only option. If Sweeps was usable, we said that the creature is doing damage to itself with this table, so crits would be rolled on the normal tables modified by 2 columns. You would still need minimum crit damage to "affect" the creature.
For example, a Sweeps against a LA troll would still need at least a "B" table result. If a "B" occurred, the crit roll would be on the Sweeps crit table, A column at -20. "C" crit would be A column, etc. A SL creature would need at least a "D" result, and would be rolled on the "B" column.
This generally worked pretty well, may have provided a bit too much benefit to martial artists but the results benefited the party so... Now the big bummer was when they would meet a group of war trolls that were immune to stun, but that's bad in general even with normal weapons
