Couldn't it be done in the UI by referencing the line/message ID, kinda like how forums "quote" the message you clicked Reply on, or 4ch references a link back to the one you're quoting?

Let a user click the timestamp to the left of the messages (or a "#" or other symbol), which inserts something like this into the reply box:

> Replying to username:

Then your message you send ends up looking like:

> Reply to username: I agree!

Clicking on "Reply to username" or just the username could scroll back the chat and highlight the message you replied to.