Make them all join in the same party that share party panel, even if they enter with 3 separate parties (or put the allies under the 'allies' section in the panel) and make it so only a number of shrines can be contested at any given time.
For example, let's say this is Saltpray beach:
___1_____3___
______2______
K_____X_____L
______B______
___A_____C___
K and L are the Kurzick and Luxon resurrection shrines.
1 and A would start controlled by Kurzick.
3 and C would start controlled by Luxon.
And the rest (2, X and B) would start neutral.
For Kurzick to capture 3, they'll need to capture 1 and 2 first, otherwise capturing 3 is locked for them.
In the same way, to capture C, they'll need to capture A and B first.
X would be locked until either B or 2 is captured.
To put it simply, you can only capture a neutral or enemy shrine that is 'adjacent' to either your resurrection shrine or another shrine you've captured.
In this example, K is 'adjacent' to A and 1, A to B, B to C and X, X to 2 and B, C to B and L, 1 to 2, 2 to X and 3, 3 to 2 and L, and L to 3 and C.
Like this:
http://img38.imageshack.us/img38/506...spraybeach.jpg
Because of this, in this map no more than 3 shrines can be contested at any given time, and sometimes there's only 2.
The 'adjacent map' would change in each map, of course. The deeper maps could have 'adjacent' maps that give the 'home team' an advantage by making it so there's always at least 3 to capture. Since the shrines are closer to them in those maps, they can get to those shrines faster.
Battles would start at the neutral shrines to control them, and then in each of the three contested shrines.
A single sneaky guy can get an unprotected shrine if the enemy teams are bad enough, but running around capturing without battle won't do, because there's less targets to capture, so people will clash more often.
Keep the rule of instant win if you capture them all for a time, and there you are, running around no longer works, and people start to actually fight it out.