Derek did the classic thing for a time travel story: he tried to change the past to make it better and wound up spawning a number of unintended consequences that may have made things worse. But then, Future!John may have inadverdently screwed up his own past many a time by sending back "Uncle Bob" (which may have completely altered his younger self's outlook on machines resulting in the mixed human/metal resistance of the series' future) and Cameron (who caused John to be eight years younger for all subsequent events plus addition confusing feelings re: machines). Jesse stuck her nose in, as well, and so have any number of SkyNet provacateurs.
The feeling I got regarding the Kaliba goons was that they were just modern-day mercs hired to do a corporation's dirty work. Winston in "Some Must Watch While Some Must Sleep" didn't seem to know anything about J-Day or machines, just that Sarah had messed with his bosses' biz. The one who electrocuted Cameron and tried to remove her chip didn't seem to be familiar with Terminators and was surprised that his boss had the schematics for one.
I'm not sure if it's that the A.I. mastermind behind Kaliba didn't know who the Connors are or didn't know that the people it was going after were the Connors. All Kaliba knew about them was that they'd been poking around Desert Cantos and soon after the place exploded, then they started poking around the employees' families and found way too much about Kaliba's dirty secrets, then Sarah killed the agent sent to grab her. They might have been deniable assets from a rival corp, spies from some government, domestic terrorists or whistleblowers for all Kaliba knew. Still, Kaliba did know they were well-armed, which makes it strange that they wouldn't deploy they Terminator for that op but would for getting Savannah.
Of course, I haven't entirely ruled out the possibility that sending the Terminator to take out Savannah was a misdirection designed to draw out the Connors, since (as I noted in another comment on here) it's awfully convenient that the info on Savannah's assassination would be on the phone of a guy who was on a completely different mission. In the end, we have no proof except her word that Weaver and Kaliba aren't in cahoots to manipulate John Henry and the Connors. I don't think a T-1001 would hesitate to kill any number of human mercenaries and security people in its own employ and destroy a dime-a-dozen T-888 to sell such a con.
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The feeling I got regarding the Kaliba goons was that they were just modern-day mercs hired to do a corporation's dirty work. Winston in "Some Must Watch While Some Must Sleep" didn't seem to know anything about J-Day or machines, just that Sarah had messed with his bosses' biz. The one who electrocuted Cameron and tried to remove her chip didn't seem to be familiar with Terminators and was surprised that his boss had the schematics for one.
I'm not sure if it's that the A.I. mastermind behind Kaliba didn't know who the Connors are or didn't know that the people it was going after were the Connors. All Kaliba knew about them was that they'd been poking around Desert Cantos and soon after the place exploded, then they started poking around the employees' families and found way too much about Kaliba's dirty secrets, then Sarah killed the agent sent to grab her. They might have been deniable assets from a rival corp, spies from some government, domestic terrorists or whistleblowers for all Kaliba knew. Still, Kaliba did know they were well-armed, which makes it strange that they wouldn't deploy they Terminator for that op but would for getting Savannah.
Of course, I haven't entirely ruled out the possibility that sending the Terminator to take out Savannah was a misdirection designed to draw out the Connors, since (as I noted in another comment on here) it's awfully convenient that the info on Savannah's assassination would be on the phone of a guy who was on a completely different mission. In the end, we have no proof except her word that Weaver and Kaliba aren't in cahoots to manipulate John Henry and the Connors. I don't think a T-1001 would hesitate to kill any number of human mercenaries and security people in its own employ and destroy a dime-a-dozen T-888 to sell such a con.