Make clipboard behave like a channel[+], like GNOME native apps do, additionally require a standard paste command to paste, then this clipboard attack will be impossible to conduct.
[+]:A sample pipe might be a good analogy for this behaviour. You cut or copy the input, send through the sample pipe, and the receiving end unpacks, receiving itself makes the sample disappear for further use. Multiple samples could be sent through the pipe, though the pipe should behave in a LIFO, no sample adding allowed after removal starts, manner if this is desired.
[+]:A sample pipe might be a good analogy for this behaviour. You cut or copy the input, send through the sample pipe, and the receiving end unpacks, receiving itself makes the sample disappear for further use. Multiple samples could be sent through the pipe, though the pipe should behave in a LIFO, no sample adding allowed after removal starts, manner if this is desired.