Don't really have an issue with it to be honest, it gives a little bit of fun to the most annoying missions in the game. Now that might be because I have shadow fall so I can summon my pets relativly unmolested. The narrow doors further in or the fact that the ambushes ignore stealth are more of an issue to me.
The trick for by-the-door upgrading is to use the pet window to select, and not click on the henchman directly. Also, prioritise your upgrades as if any second you're going to be jumped on.
For instance, with Robotics I want my Assault Bot double-upgraded for the attacks, followed by the Prot Bots single-upgraded for the heals. After that it's a striaght run through on the Drones.
I do occassionally get jumped (especially on the speakeasy, casino and some office tilesets) but I do usually survive.
By far my most annoying point.. the healing of the protector bots. They serious dont know WHEN to heal my other bots, just randomly they seem to heal them (or not). No mather what 'mode' i put them into, they just refuse service. I noticed they hardly heal eachother, quite weird.
Second place, Assault bot flame trower, slow animation, wrong direction. Though without the lvl6 upgrade they wont use it 
And offcourse, the happy cave-missions. They keep trying to run around, instead of just face the fact that cant move any further because there are 4 bots infront of them.
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(50)MaceX/(50)Encore
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The best thing for summoning is to turn 90 degrees when you go in so the door isn't behind your character. When you can see the door from another angle, you are less likely to click it. When you can't see the door as it's behind you...virtually any area of the screen can be seen as 'door' 
Zap has it right too, use the pet window, which is great, the only problem with that, is you do all your upgrading using the pet window...then have a mind burp and click on the most threatening npc to attack! Oh dear...forgot the bloody door!
...my tip, take a few steps forward and turn 90+ degrees sideways, then summon and buff!
There is if I remember correctly a keybind that will allow you to preform a 180 degree turn. Can't be bothered to look it up at the moment. But if you used that you would be facing the door and outside the click box.
Well thanks for your opnions guys, I will try it out. But that still doesn't excuse for all the aggro they soak up on these bank missions, any1 got any ideas. 
Stealth or Invisibility.
I really should do something about this signature.
The simple trick, make a keybind to (for example) numpad 7/8/9 to change the 'mode' of all your pets into passive/defensive/aggressive.
The moment you click the place for them to drop, start wacking numpad7, they will pop into passive straight away. This way they will never draw any agro as long they are out of range of the mobs (just like yourself actualy :P)
Works like a charm for me.
50)Sinergy X/(50)Mika.
(50)MaceX/(50)Encore
Sign the petition, dont let CoH go down! SIGN!
hmmm, those do work, but it's the problems put together that really does get bon my nerves in team missions, anyway thnx for your tips guys.
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Stealth or Invisibility.
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Doesn't work, if the ambushes agro on you they will always attack you, only way round that is Phase shift of PFF neither of which I have 
And the ambushes in Heists are the main reason I have avoided them since about lvl12-38 I do them if I need a new contact not otherwise. My Brute finds them fun.
Yeah, brutes would like that now wouldn't they, all that fury biuld up against weedy little police officers.
I wish some1 would do something about this, this problem is most frustrating in the entrance of a bank, you are put in a small and cramped room with guards near you, and when you summon your henchman you either click on the door by accident and you go out, killing all pets you summoned inside, making you have to summon them and upgrade them all over again. OR when you do summon your pets you aggro the guards and the fight starts with you off guard(this ticks me off in team missions). Post your opinions here if you wish.