Why would Pops help build Cyberdine instead of just destroy it?

What is Pops' mission?

To protect Sarah Connor. Everything else comes second to that.

Pops' mission taking the long way to the future is to prepare for their arrival so they can work together to destroy Skynet. He needs to secure a location for them to work out of, stockpile guns, ammunition, and explosives, and to scout out ahead of time so they know where they need to go. So far so good: this is a relatively safe mission for a killing machine. He is unlikely to render himself unable to protect Sarah Connor in the future.

Now consider what could happen if he striked preemptively at Skynet.

• As a T-800 with no confirmed other terminators nearby to stop him, he could inflict serious damage to the facilities and possibly even achieve mission success.

• Skynet is located in a major population center. This is not rural America where a T-800 could single-handedly destroy an entire town before anyone know what was going on. With millions of people in San Fransisco and the surrounding area, there will be police, SWAT teams, National Guard, and plenty of weapons that would eventually overpower him. He is a lone terminator, not a terminator army.

• During the bridge scene, remember when he says (paraphrasing) there are too many cops and not enough bullets: attacking would jeopardize my (primary) mission and is a tactical failure." The same is true of attacking Skynet: while success is theoretically possible, there is an unacceptable risk of failure which would endanger Sarah Connor by virtue of Pops being destroyed or severely damaged. In other words, attacking Skynet might cause him to fail his primary mission.

• Finally, he may have known about John Connor's secret: remember how Pops reacts to John in the hospital parking garage. If he was not aware, there is still a risk that somehow future Skynet could have delivered a terminator to protect "infant" Skynet. If he was aware, then he certainly knows John is protecting Skynet. Either way, there is a nontrivial risk that another terminator is present incognito which would pose a significant risk of damaging or destroying Pops, causing primary mission failure. Remember, there are terminators more advanced than the T-800, but nothing we know of less advanced. Pops best possible chance against another terminator without help is 50% and it goes down from there.

The terminator is an infiltration unit, designed to blend in to allow it to strike from within (as long as everyone is a 6ft Austrian, but lets not go there). Knowing when Sarah and Kyle were due to arrive in 2017 it infiltated to allow it to both gain detailed knowledge of the facility (to aide destruction via explosive), and to allow it to program access for Sarah and Kyle to the safe room, for when they do.

The key time for them is just before skynet/genisys becomes active, a strike earlier isn't guaranteed to be effective, and may make things worse, as we've seen by the T5000 changing time by affecting John Conner.

The Pops that helped build Cyberdine was before he was reprogrammed and sent back in time to protect Sarah as a child.

At that point he would be a terminator following the orders of the AI Skynet. He would have no reason to destroy Cyberdine.