By far an excellent review / suggestions. I do have some observations to offer though:
Agree with your suggestions.
As an observation a Pacifist race in an SG first contact team will be problematic. These are combat teams that are part of a combat arm. I could see them in a follow up research team, but as part of a first contact team, the leader who already has limited resources, being out of contact to a great degree, has one less gun, one less person to take a watch shift, etc.
No observations - really good ideas
Agree with the Ma'tok staff, but I would not replace the TAC vest with Jaffa armor. There are many reasons units are in "uniforms", the big one is identifying friend from foe. A Jaffa in Jaffa armor carrying a Ma'tok walks into a peaceful village for first contact... the results pretty predictable. Also these are MILITARY units, your uniform selection outside of certain special forces units is not up to your discretion. If they could be worn separately, I could seem them wearing the collapsible helmets though.
I am on the fence regarding them getting proficiency in other weapons - by their nature they will want to be the most effective combat assets that they can be. If you are going to let Humans get Jaffa weapon proficiencies, there is no reason Jaffa shouldn't be able to get human weapon proficiencies (I think I just talked myself into that )
I don't know that I agree with every Tok'ra automatically getting Jaffa weapon proficiencies, though I agree they should have access to them.
Agree! Great suggestions!