For these specific missions where you have to destroy a depot, I destroy them with my ship. When you are within the atmosphere of a planet, no sentinel spaceships are deployed, so you are pretty safe if you remain inside of your ship. You will still get the cargo that the depots contain (so long as you have inventory space in your ship). After you destroy the depot, simply fly away from the sentinels (but remain in the atmosphere) and they will eventually back down (unless you get a 5 star wanted level - see below).
If you decide to venture on foot, some things I've noticed when being chased by sentinels is that if you go inside of any building, they will not attack you. In fact, they can be in the building with you, and they will still begin the "searching" process with the countdown timer. If you let the timer tick down, you can escape them. I think the reason for this is because when you enter a structure, it forces your character to put away their multitool, leaving you defenseless. I think the developers of the game realized this, and as such, made the sentinels stop attacking you.
If no buildings are around, and you are taking some heat, use your terrain manipulator to dig a tunnel and get away. You might have to dig quite a bit, but the sentinels are generally not smart enough to follow you into the tunnel (most of the time they can't even get in it).
If you want to fight them, I've found that so far a scatter blaster is one of the best weapons against them. It can nearly one-shot the small flying sentinels if you are close enough to them, and as for the Walker units, it can destroy their leg armor very quickly. After you destroy the four leg armor pieces, you are able to begin shooting the Walker head to destroy it. I've found myself destroying Walkers in as little as a minute. If you are taking a lot of damage, you can dig a tunnel (remember, the sentinels aren't bright enough to follow you into most tunnels) and allow your shields to regenerate or use some resources to recharge your shield.
From an old answer that I've posted, once you reach a "5 Star" rating with the sentinels, they will not back down, even if you try the building trick (although they won't attack you in the building still). The only way to lose a 5 star rating is to fly out of the atmosphere of the planet you are on. This will in turn place a 1 star level on you, and a sentinel starship will begin to hunt you down. There isn't much you can do to run away from the starships. You can fight them, but this will just raise your wanted level further. You either need to dock your ship on a freighter/space station to lose the starships, or land on a planet again. It may be hard to reach a freighter or space station however, since you cannot engage your pulse engine when you are engaged with the sentinel starships.