Edea's SeeD weren't the people that took baby Squall to the orphanage, SeeDs did not exist at that time.
Squall (Time Traveled, Teen) told Edea from the past Garden SeeD .... Young Squall was already there.
It's like a repeat of history.
During Time Compression...
Ellone sended both Rinoa and Ultimecia further in the past
(She could not reach the Laguna era at some points, since she's limited to the time travelled back)
When she sended Ultimecia in the past, Squall already defeated her since (Due to time compression, time stopped, so Squall and the others journey to the futur took an instant)
So then Edea took the sorceress power...

Squall got lost in time compression, but Ellone sended Rinoa in the past (That was compressed), so Rinoa found Squall laying down.
She took him in his arms and Ellone took both Rinoa and Squall back to the present.
The end.


That's alot to swallow, I hope it's not confusing and clearing up theses issuses...

Point is, Squall got to the orphanage by someone else than SeeD.