I saw it more as a message. I think they probably knew she wasn't on the boat at the time, but are showing them that they could end them at any moment if they so please.
Not that I think these people give a shit, particularly Greta. That girl is fearless. If anything, this is just Streisand Effect for their flotilla and her message.
The Zionist Regime is amazingly out of touch. I know on some level they don't care, but even their propaganda targeted at populations of allied countries is bizarre and making their audience second-guess them.