"Just like he smuggled Morgause out instead of letting her be killed. Maybe it was his sweet revenge on Uther, by keeping Morgana's powers secret. As much as trouble bad magic users may have caused, lots of innocent people and children too died in Uther's hand. Deep down in his mind, there ought to be some grudge/ grievance/ sadness about that."
Morgause was several years older than Arthur, so Gaius smuggling her out of Camelot had nothing to do with the Great Purge. We don't even know if Uther was king yet when Morgause was born. Sadly, the showrunners never came up with an explanation why Gaius gave her to the High Priestesses.
It was also said that Uther was led to believe that she had died but not that he was the one who wanted her dead as a baby. I would imagine that since Vivienne had an affair with another man while being married to Gorlois (if she was already), Gaius smuggled her out to prevent the entire family from social harm and due to the fact that Morgause had magic (in case her magic was already shown when she was only a baby). Maybe the Old Religion claimed Morgause even before she was born and made Gaius swear to bring her to them while everyone else thought she died.
Whatever happened, Uther had no reason to wanting her dead because of magic since the Great Purge and his hatred only started after Arthur's birth and Igraine's death.
I agree that Gaius probably held a grudge against Uther and actually wanted to punish him, but not in the first seasons already. To me it seemed that he became indiffierent towards him since season four and maybe even wanted him dead. Shame. In the first three seasons, Gaius still seemed to care. Not to mention that he himself wasn't exactly innocent in regard to the Great Purge and maybe also in regard to Morgause.
ReganX, you may be right. If so, it would have been a good idea if different motivations on Gaius' side would have been mentioned/hinted on the show. The way it was presented to us we have to think that Giaus only feared that Morgana would be killed by Uther.