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.