"My husband went to the Eggmine and never came home. He knew the mine was closed by you foreigners and guarded by the Legions, but we had no fresh kwama eggs. If you want to help me, go the mines and find out the truth."
-Widow Vabdas
Vanilla MW gives you the option to side with the Legion, and (optionally) helping the widow. However, you cannot directly support the anti-Legion sentiments in Gnisis. I have started writing dialogue for a small personal mod to give anti-Imperial player characters who do not join the Legion that freedom of choice.
You start the quests by talking to Hetman Abelmawia. If you're Archmaster (or Hortator) of Redoran, he'll tell you about the murder of Mansilamat Vabdas, and humbly ask you to visit the widow. You'll basically follow non-Legion versions of the first two Legion quests - http://www.uesp.net/wiki/Morrowind:Widow_Vabdas%27_Deed and http://www.uesp.net/wiki/Morrowind:Gnisis_Eggmine_%28quest%29 - with some dialogue tweaks, after which the Hetman tells you that House Redoran should be the ones handling security in Gnisis, not the thieving, murderous and incompetent Legion.
Suggestions are welcome and appreciated. And yes, it's compatible with Great House Dagoth.