The Emancipation Proclamation said nothing about the equality of blacks as a question of government or non-government realms. It simply said that from X-day forward, as the Union army reclaimed territory from the South, any slaves in those areas would be freed.
It didn't actually even make slavery illegal as technically someone in an area where slaves had been freed could simply import new slaves from areas where they were not yet free.
In fact, there were areas already under Union control before the Emancipation Proclamation went into effect that were exempt from the EP and so those slaves were not immediately freed). At the time, the EP was ridiculed by many for only freeing slaves over which Lincoln had no control and refusing to free those over which he did control. It actually took longer to free the slaves in Delaware (a Union state) than in Mississippi (a Confederate) because Delaware was excempt from the EP and slavery remained legal until the passage of the 13th Amendment.
As for equality I have no doubt that Lincoln didn't view blacks as equal. Hardly any of the hardcore abolitionists thought of blacks as equal. I do'nt recall what his position on what eventually became the 14th Amendment was (which is when blacks were given equality at least in terms of government treatment).
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