Yeah, as far as I know tModLoader currently doesn't have any sort of support for replacing sprites inside of mods. I am working on something that will eventually be able to do that, but it's not really done yet.
For now, one way to do this, is by extracting the mod using tModLoader's built-in extractor, modifying the sprites, and then repacking the whole thing. Unfortunately I ran into some annoying complications, so things got a bit convoluted... Basically, Thorium is a little bit broken, it has a bunch of invalid TileObjectData entries, so if you rebuild it using the latest tModLoader 0.11 it won't work. However, if you build the mod in 0.10, tModLoader 0.11 will ignore these errors.
So, anyway, the point is I got Thorium converted using hq2x, here is the download:
Thoriumhq2x.zip
And if anyone wants to do this again, here is a rundown of the whole process: