TomiF- I havent played The Gate for awhile now but it is still one of my favorite decks and I always haunt this thread.

Anyway Re: Hivemind combo and your SB in general, I would suggest some combination of 3 surgical extraction/extirpate to start and then a playset of either sundial of the infinite or possibly even lich's mirror.
I know both are extremely narrow and sundial is probably the better (although more narrow) of the two but humor me for a sec. The upside to these is both are essentially free to cast and uncounterable answers to hivemind when they SNT so they are every bit as fast as the HM players combo and both are reusable. They also both allow you to still completely tap out in your turn since the HM player will be casting SNT during his turn.
The mirror can even win games against aggro decks like zoo if they are depleted when they reset you. I was actually surprised by how effective it can be. I have not tested very extensively with the mirror though so this is mainly theoryhammer here but in the absence of really any other options I would look to these two if you expect to encounter HM in force as splashing colors is not an option.

The downside to lich's mirror of course is that you start at ground zero again so if the HM player does have multiple pacts they can just use 1 to reset you and follow up with the second pact to kill you next turn. This though requires them to have a 4 card combo which isnt always that likely, especially with the amount of disruption The Gate maindecks.

There really isnt a good answer to leyline for The Gate that I am aware of but at least these two options would allow you time to get Dystopia online to remove it.

Lastly you could consider phyrexian metamorph for the SB too if you are really that worried about leyline since it does answer emrakul/progenitus without targeting. Personally though I would take the above suggestions and take my chances with leyline.
Anyway hope I gave you a few ideas. Cheers.

Edit: I actually just thought of another option that could possibly work out, maybe with some form of acceleration i.e. rits or mox...trinisphere
In fact I wonder if this could find a place MD in The Gate since many of this decks spells already cost 3-4? It obviously wrecks countermagic and any type of tempo oriented deck. GftT players could opt to run Dismember and/or Snuff Out instead and Cabal therapy would remain uneffected lategame due to its alternate casting cost. Vial effects would still function but The Gate has plenty of answers to creature based strategys.