I think the key parts of the Synthesist rules are -

Spells such as banishment or dismissal work normally on the eidolon, but the synthesist is unaffected. Neither the synthesist nor his eidolon can be targeted separately, as they are fused into one creature.

This indicates that, although the Eidolon can be affected by some specific summoned-only spells, nothing else can target the pair separately. And Control Summoned Creature will ONLY work on the Eidolon, not the Summoner.

As a GM, I would rule that the spell does very little. I would allow the caster to dismiss the Eidolon, as the Synthesist normally could, but there would be no other effect, and the Synthesist could then resummon it as normal.

I think the key parts of the Synthesist rules are -

Spells such as banishment or dismissal work normally on the eidolon, but the synthesist is unaffected. Neither the synthesist nor his eidolon can be targeted separately, as they are fused into one creature.

This indicates that, although the Eidolon can be affected by some specific summoned-only spells, nothing else can target the pair separately. And Control Summoned Creature will ONLY work on the Eidolon, not the Summoner.

As a GM, I would rule that the spell does very little. I would allow the caster to dismiss the Eidolon, as the Synthesist normally could, but there would be no other effect, and the Synthesist could then resummon it as normal. Dismissing would take a Standard Action on the part of the caster, meaning they likely wouldn't be able to do it on the round they cast the Control spell.