Consider this situation: You have a minor (or weak major) near you, which you trade with and dont want bullied by the Drengin. You are not sufficiently advanced in diplomacy, or dont have a good enough relationship, to make an alliance to them, but still want to make sure no one can conquer them. So then you go into the diplomacy screen, and annouce to them that you guarantee their independence. This should have two effects:
1) If someone declares war (DoW) on them, you should be presented with a dialogue prompting you to honour the agreement and DoW on the aggressor, just as if you had an alliance with them.
2) The AI should take 1) into consideration before a DoW, just as it does if an alliance was present.

The difference betheen an alliance and a guarantee of independence, would then ofcourse be:
1) It is a unilateral treaty, so you can guarantee someones independence, even if they hate your guts.
2) It only binds one way.