There are only four cards in the current Modified format that have the Safeguard Poké-Body: Altaria from Deoxys, Dewgong from FRLG, Ninetales from Hidden Legends, and Dustox ex.
Feraligatr ex and Medicham ex don't care about the first three, since Overpowering Fang and Wise Aura both do the same thing. Each of their Poké-Bodies shuts down Safeguard, rendering it useless.
Dustox ex is another matter, since there is no card that can shut Safeguard off (well, besides Goop Gas Attack, which is beyond illegal). For him, I use Mr. Mime Ditto, which can OHKO Dustox ex with Silver Wind. Mew ex works in the same way. It does have 30 more HP and that neat little Poké-Body. Against a fresh Dustox ex, he can't OHKO it, which is fantastic.
Then again, you might not consider Ditto or Mew ex a counter for Safeguard since they really are only supposed to come out specifically if Dustox ex is on the field.
As far as everyone else goes, you can shut down Altaria's Safeguard using Battle Frontier (like anyone plays Altaria anyway). For everyone else, all you can do is hope they attach Energy Root to whatever's got it.
If they re-released Goop Gas Attack, we'd have so much fun with it.