[RPG] How to make Will saves using Intelligence

Yes.

Unconscious creatures get to make saving throws as normal, with the exception of having a -5 Dex modifier. From the Condition listing:

Unconscious: Unconscious creatures are knocked out and helpless. Unconsciousness can result from having negative hit points (but not more than the creature's Constitution score), or from nonlethal damage in excess of current hit points.

and further from helpless:

Helpless: A helpless character is paralyzed, held, bound, sleeping, unconscious, or otherwise completely at an opponent's mercy. A helpless target is treated as having a Dexterity of 0 (–5 modifier). Melee attacks against a helpless target get a +4 bonus (equivalent to attacking a prone target). Ranged attacks get no special bonus against helpless targets. Rogues can sneak attack helpless targets.

[Helpless creatures are subject to coup-de-grace]

Nothing here limits the availability of saving throws. Neither do the descriptions of the Saving Throws themselves:

Fortitude: These saves measure your ability to stand up to physical punishment or attacks against your vitality and health. Apply your Constitution modifier to your Fortitude saving throws.

Reflex: These saves test your ability to dodge area attacks and unexpected situations. Apply your Dexterity modifier to your Reflex saving throws.

Will: These saves reflect your resistance to mental influence as well as many magical effects. Apply your Wisdom modifier to your Will saving throws.

In absence of primary rules forbidding saving throws to unconscious creatures, they aren't.

If you can meet the prerequisites of prestige classes by your previous gestalts, than it is reasonable to take Beastmaster as soon as possible. I assume you are going to finish your Convoker advancement, so the character would look like that:

Commoner 6 // Convoker 6 // Beastmaster 1

At the first level Beastmaster provides boost to your effective Druid level, so it will be a companion of 4 level Druid from the spot. I dont realy think you'll very much need any more levels in Beastmaster as it stacks with any companion advancing classes, and they have better class features.

From now on I see two options:

1. Take Druid for spellcastng, if you have room for it in your actions. Five levels will give you access to highest level spells even without that level lost due to Beastmaster. You also will have room for adding more prestige classes at those five levels later, as Druid is a regular class. Finaly, as a regular class, it has no prerequisites. It results in:

   Commoner 6 // Convoker 6 // Beastmaster 1/Druid 5

2. Stack some other prestige and maybe regular classes with nice class features wich progresses your animal companion. I'd consider Wild Plains Outrider, good class with quick advancement and ability to make a full attack after mount's single move. Two remaining levels may be of practically any class wich progresses your animal companion, probably those of a Beastmaster or even some regular class whose class features you like. It results in:

   Commoner 6 // Convoker 6 // Beastmaster 1/Wild Plains Outrider 3/xxx 2

I can't realy wrap my mind around Animal Ally feat mentioned by Chemus. I feel like, depending on your DM's judment, it may be quite usefull, but when to take it is a question I can't answer. Beastmaster and Wild Plains Outrider are both from Complete Adventurer.