MagisterCultuum provided a lot of good advice. I would add that I generally build my Altar in a city near my cultural boundaries where I want more culture, not in one of my core cities. It is easy enough to walk the GP to the city to build the Altar. It is also easy enough to walk defenders from the core cities out to my Altar city.
One asdditional tip is that the final stage of the Altar has a long build time. I would try hoarding a few Great Engineers to hurry its production. Obviously hou have different cities with Engineer Specialists and wonders that provide GP points for Engineers separate from the cities that are pumping out your Great Prophets. This is also a good tip if you are planning to build the Tower of Master for another victory method.
I've never seen the ai civs come after me when I was building the Final Altar like what happens when you go for the Tower of Mastery. Maybe it is like the Magister says, it depends on the civs remaining in the game.
I find it is very easy to get an Altar Victory playing as the Elohim, especially Einion Logos.
As Mesix said, it is great if you have GP Engineers to aid in building the Final Altar. You can get them more easily with ROK/Tablets of Bambur in one of your cities, as well as other Wonders.
Two other good strategies:
1. Don't obsolete your Soldiers of Kilmorph if you have ROK. They are great for hastening the completion of the Final Altar.
2. Time the building of the Tower of Divination so you can use the free tech to get Omniscience. That is the one necessary for building the Final Altar and it can take long to research.
I will also try to specialize with my cities if I can. One for producing military units, Great Commanders, etc., One for producing Science/Sages, One for producing Great Engineers, and one for Great Prophets and the Altars. It isn't always easy to do during a game, but if you can, it makes the Altar Victory one of the easiest ways to win the game IMO.