It could be as simple as making the orb spawn once every 2/3 minutes or just removing it entirely for Spirit Watch. In regards to physical movement skills giving some classes advantages: so what? Classes with teleports have unique z-axis mobility on all maps and classes with stealth can commune in Silent Storm while using it.
Skyhammer would require a bit more, but if the panels become solid (and unhittable) and asuran shield walls appeared around every edge then only the hammer itself would remain (unless it got deleted, then the map could just have lots of walkways and jump pads.) It could be changed to a commune that then automatically fires at either the cap points/a selectable cap point/all enemy players etc. and takes 20+ seconds or so to recharge.