Open C:/Documents and Settings/"User"/Local Settings/Application Data/Ironclad Games/Sins of a Solar Empire/Mods/The Mars Effect/Game Info/GalexyScenarioDef

Use Notepad to open the file.  Scroll down to about 70% of the way down the file's scrollbar.

Change this:

pirateRaidDef
  arrivalDelayTime 6.0
  minSupply 1
  maxSupply 350

To this

pirateRaidDef
  arrivalDelayTime 6.0
  minSupply 1
  maxSupply 300

It worked for me, 18 hours into a 5 star 400planet system that started crashing during severe pirate raids after installing TME mod

Now I can resume playing normally with seemingly no issues during pirate raids.

Thanks.