Sneaking around and not engaging during an invasion is dwarven if you're rigging the building for demolition.
On modded servers you could even make some things look like accidents.
Punch holes in containment buildings, overheat fission reactors. All evidence of the tampering erases itself.
Crosswire IC2 powernets of different voltages, or leech power from a rival with particularly high generating capacity.
Rewire sorting systems.
Cut coolant lines on things that fail catastrophically.
There's really nothing hostile besides mob-funneling you can do in vanilla that isn't obviously enemy action.
As far as open warfare, vanilla has only a few available hostile actions.
I think I can even list them exhaustively.
Liquidspam, removing blocks (strategicly or razing entire buildings), encasing things in awkward materials (obsy), funnelling mobs to them, killing/spawncamping with personal weapons, removing valuable items from chests, killing/stealing livestock, fire (situational), making noise, TNT, silverfish (kind of a subset of mob funneling).
In modded servers, you have, in broad strokes:
E-war in its many forms, various explosives and delivery methods, environmental damage (radiation/magic equivilants, etc.), MANY kinds of subtle industrial sabotage, automated demolition, more variety in personal combat, etc.
I guess all the servers worth invading are vanilla, but I'd like to see Bay12 fighting an actual industrialised war (with the competitive RND and investment in counter-counter-countermeasures to the Nth degree that implies) against other people, and the only game I can see that happening in today is heavily modded Minecraft.
Actually, last night I designed in my head an automated omnidirectional artillery/flak gun that should work in MC and be fairly compact. (it would need CC and either RP or something else that adds something like jacketed redwire; and while I can pseudocode out the turtle and control console instructions, I have no experience with CC programming (I think it's lua?))
Are there really no Technic or whatever servers out there worth invading? Victory is always more fun when it involves a battle of wits, a clever bypassing of defences, and a radioactive hole in the ground.
Regardless, if we get a cohesive Bay12 faction ready to go to war on a vanilla server, I'm interested in helping.