That works. The | prompt is a continuation prompt telling you the input is incomplete. So, you can just keep typing, e.g.
?- <return>
| write(hello).
hello
true.
?-
Another popular trick if you use , (comma) rather than . (dot) by accident is to add true., e.g.,
?- write(hello),
| true.
hello
true.
?-
On some installations pressing ^C (control C) and a (abort) also works. It depends on the input method (plain terminal, GNU readline, BSD libedit, embedding in Emacs, ECliPSe, etc.).