Last night I got a text from a girl I've slept with on 2 separate occasions.
I hooked up with her the first night we hung out, than hooked up with her twice a week after. Now about 3 weeks have gone by since we've seen each other.

Have you made any attempts to get her out during the span of 3 weeks?

She's been busy with school and work so I didn't assume anything, instead I decided to give eachother some breathing space.
A week after the second lay we texted almost everyday but a week after that she became distant (very late texts and spaced our conversation)

This could very well be a situation of not striking while hot. Again, I am curious to know if you've made any attempt to take her out?

Out of the blue she messages me saying
"Is it okay if we just stay friends, I think we've been going about things all the wrong way and that's not me, I want to get to know you more and let time tell what happens"

Looks to me the attraction has waned - this could have been a result of poor logistics, but regardless if she was really feeling things she'd have made more of an effort to make herself more available, though admittedly I don't know how your conversations went down. For all we know you were hounding her to hangout in those texts (or not), or having poor boundaries, making yourself too available etc). There's a lot of info missing here.

Now I took this as "I'm not romantically interested in you, but you're cool enough to keep around"
I'm I in the wrong for assuming this and how do I go about rejecting the friendship? I've never been in this situation so I'm not sure what the proper action to take is..

A week after the second lay we texted almost everyday but a week after that she became distant (very late texts and spaced our conversation)