hey mate
the text was a mistake. From what i remember of the other thread and what you are saying now, you were never sexual or insinuatingly sexual. Which is on itself ok. And all of a sudden, kablamo, there you are. Sexual, wrapped in a joke. This is awkward, hence why she asked: "how did we get there?". The joke is not congruent with the entire interaction and also not with the image she has of you.
What you needed to do was, instead of the texting, tell her face to face: "hey, i want to get to know you better, lets go for a coffee when i am ready with my work." or something like that, someplace you can talk.
But you didnt. I think, to solve this, perhaps a bit of straightforwardness would be in place. Now you can text her, because she might not be coming back for some time

and i would text something like this:
"Hey, i am sorry. the threesome thing was a joke. A bad one it seems. What i really would like is to get to know you better. i think you are quite attractive and i want to learn more about you."
Something like that. A 'no' you have, a 'yes' you can get. What you sent her was a bit awkward, but IMO this is not a total loss. I think you still have a shot. If you stop hiding.
good luck!