The question is not wether Tanya is Evil. Well, in a sense it is, as despite in the later part it more turns into an action/war anime than the original existential premise, in its core the purpose is the confront religion, and the actual existence of a god, with an atheist.
The show mostly do a good balance between the two point of view, although in certain episodes they loose this for the favour of this or that.
A problem can be that the series relies on knowledge of wildspread arguments between religious and atheist speakers.
To start with, Tanya IS evil BECAUSE she/he (watch episode 2 to see) does not have faith, according to the religious argument. Or if Tanya has faith, it is distorted, thus is the worshipper of Satan. It is a misguided argument full of prejudice, but that's the actual use of the word in religious circles.
Now Tanya is obsessed with "the end justifies the end", and is pretty selfish, though that selfishness is directed to living in peace, while Being X, aka. God is The Lord of Hosts from the Bible, and pushes the whole world in a world war in the hope of being worshipped. So while this Being X is(?) the creator, also looks a bit incompetent, lacking understanding of its own creation.
The biggest flaw of the show is, it reaches nowhere. There's no resolution for Tanya, no dealing with Being X, no dealing with faith. The whole thing simply deteriorates into oblivion. And throwing in at the end a LITERALY called Mary Sue? What was that for?
Well, you could argue, that Tanya is actualy Satan in God's hand as tool to cause humanity to believe... But that's preaching, as has nothing to do with Tanya itself. Who you know, the audience should be cared for, being the POV-character and all.
