1. How to deal with lolwebul groups effectively
Groups that create a visible profile ingame get crushed within two weeks of their creation. Let them build up and be destroyed by the CCA. They will bring it upon themselves and if they manage to survive, it presents a challenge for the CCA to deal with in the long term. I started off as a mingerebel that spawned a random cinder block on a bridge overlooking a street and dropped it on to a CCA unit's head. My character was caught and beaten and that started me on the road of actually developing a character for resistance RP (and thus Third Eye was born). It's through failure that we learn but if we start targeting groups because "your rp is shit and I don't like your group" then HL2RP will fail in it's entirety. Encourage players to be better and not to follow a bad example by setting a good one.
As bad as it sounds, you have to encourage people to RP as a rebel by getting them into entry-level positions. Whether they're a thug or a prostitute, it doesn't really matter. Obviously if people hoard AR2's and decide to kill every citizen who walks into the scummy parts of town then yes, they should be destroyed ASAP by the CCA.
2. Perhaps an official resistance? As to make sure that it all forms of a resistance can't just vanish.
I haven't really seen official resistance groups done well on the City server, in the past and on other servers it just seems to be collecting guns and ammo and then having a massive onslaught at the end of every week with the CCA. An official resistance group needs to facilitate and encourage the growth of passive RP against the Combine occupation without bringing dumb violence into the equation. An official resistance group (if implemented and managed well) won't even need a gun or vest in any members' inventory. There are thousand more ways to subvert and disrupt the Combine than shooting at them.
3. Someway of ensuring they aren't instantly killed off by the CCA.
In the end it's up to the discretion of the CCA to decide when enough is enough. They're the most resourced and well-supplied faction in HL2RP and if they want an enemy to fight then the players will have to use common sense in situations where the fate of rebel RP is in their hands.
"We have all of the members of a group up against a wall, some of them had guns, others just had handheld radios and others were unarmed but are associates. Let's kill them all to send a message." - a classic situation of how the CCA would work but in practice for HL2RP it's just going to piss people off and put players off from making/associating their characters with rebel factions.
"A citizen just came in and gave us some contraband, now we're putting him in the incinerator. Who knows where we got the gear from?" - another situation which happened too frequently; people reporting crimes/handing in contraband/giving information and getting punished for it too harshly. Again, you would probably not risk it if you were actually in the CCA but in the long run it is just not worth killing one character over something so petty.
The CCA should be employing secret police tactics more often (ones which don't result in a PK on the first offense by a citizen) like forcing citizens to become informants, torturing for information (yes, this happened a lot but it seemed to be over minor details after which the characters involved were PK'd - what did you really gain from it?) and several other tactics which can be also used.
i can't think of many ideas for the resistance, as i have hardly ever played a resistance character (and when i did, it was undercover unit so...).
It's the responsibility of everyone on the server to make sure there is not an imbalance in CCA vs Rebel RP. If one starts being better than the other, guess who all of the players are going to join up with? Make them as good as each other and you have a perfect combination.