If they mine the entrances to buildings (especially the all important barracks) there is a simple solution. Go to another important building OR put the beacon right outside of the building. It might not do as much damage, but it's still a pretty good blow. And also, if you're in a small game, the enemy is too buzy trying to find a good way to destroy you.As for GDI, if they mine the tunnels just be careful not to set the mines off. If it's a small game they probably won't even bother to mine the tunnels.
And also, even though you can dodge obelisk fire, it's still a lot safer to shut down the obelisk. I'd recommend shutting it off over dodging its fire (although dodging it can be pretty fun).