It's just "e minor". The C# sounds funny because it clashes with the b5 of the F#mib5 chord and the b9 of the B7b9 chord, both of which indicate a C natural.
A really simple way to think of E as a tonic minor is this:
E, F#, G, A, B, CorC#, Dand/orD#, E
The first five notes never change. Both versions of the seventh are valid over altered V chords (in this case the D would be the #9 and the D# would be the 3rd). The lower of the two sixths is indicated over the ii-7b5 to V7alt part of the progression, but over the tonic chord players may choose to play raised 6th and 7th (melodic minor), flatted 6th and 7th (pure minor), lowered 6th and raised 7th (harmonic minor), raised 6th and flatted 7th (dorian minor), or even lowered 6th, lowered 7th andraised 7th (I like to call this "bebop minor" although other people use this designation for another scale).
I think of the 6th and 7th in the instance of tonic minor progression as "toggle tones", meaning they can either be raised or lowered like a light switch depending on what color is desired. Hope this helps.