This advice applies to the current version, 6.010, and may or may not apply to previous versions and upcoming versions. Most specifically, Guard Posts are getting buffed and changed in 6.011 as soon as tomorrow.
1). I personally don't bother killing the wormhole guard posts on difficulties 7/7 unless I have plenty of frigates from the Fallen Spire Campaign or Implosion Artillery Spirecraft from the asteroids (rather useful against eye-happy opponents), or perhaps an Artillery Golem but even then I would forget. My singleplayer games tend to go on too long and progress too slowly, so I have Spire Civilian Leaders on in order to encourage me to play faster, up to a point at least.
I have two basic neutering strategies: 1). I'm there already, clearing out everything guardpost wise except special forces, leaving warp gate up. I often wipe Ion Cannons before proceeding to neuter. 2). I'm busy building stuff back at home (like starships, high mark fighters) and rather than have my fleet sit idle, it's better to give them something inexpensive to do before the recently alerted planet has had an opportunity to build up.
For the second strategy, I first send in my fighters to hit medium hulled guardians, pull back, reinforce to full, then send them in again with bombers and frigates to hit a few of the softer targets, avoiding gravity guardians and the like. When I do this the occupying forces are usually under 100, up to 200 or so, and it's a mark 3/4 planet. The fighters are expendable, but the bombers and frigates aren't, and by taking out targets of opportunity now, there will be fewer guardians to harass me later when I come in full force. There's variations to this depending on the AI's bonus ships, prompting certain starship focuses on the medium and above AI personalities. Unlike the first strategy, I'm just interested in getting in and out as quickly and costlessly as possible. This hit and run does have the unfortunate tendency of setting loose some fairly nasty threat, which is why I only hit mk4 systems with low level fleetships when they have less than one hundred ships in system. Later on when I have my starships and various stuff I do tend to be more completionist and aggressive. Generally speaking, though, this is what I do in the first hour or so of the game, when I can't afford the power or resources to build the forces to do a full assault on a nasty system. Oh, and half the reason I'm doing these raids is to take out the tachyon guardians, making it easier for my scouts or cloaked bonus ship type to wreak havoc.
4). Speaking of choke points, there are quite a few strong reasons to go with a sole target for incoming waves, especially in a co-op game. However, if you leave multiple wave gate points of ingress into your space, the waves will be both smaller and more frequent, and this is before you take into account the 5 AIP cost of knocking off warp gates. If you leave some systems in front of your heavily fortified choke, you'll generally have the same total ships come in, but in more manageable chunks. If your AIP is low, you can often get away with an edge of system logistics center, sniper, spiders, and riot starships flown in at the last minute. You'll micro the riots a bit to keep them out of range of hostiles, but generally your goal is to engine damage as long as possible and buy time because your fleet is busy elsewhere and you've invested in a blob strategy (munitions boosters, snipers, plasma siege starships) instead of high mark raid starships, stealth battleships, eyebots, etc...
