This is not something Geany can do anything about.
Right to left text is not supported by the Scintilla editing widget on the GTK backend used by Geany. As its documentation says:
"Scintilla only correctly displays bidirectional text on some platforms. Currently, there is experimental support for bidirectional text on Win32 using DirectWrite and on macOS using Cocoa."
and even on those platforms
"bidirectional features are experimental and incomplete"
Exactly how bidirectional text displays in Scintilla is undefined on GTK backends and any behaviour is luck from the behaviour of system libraries (Pango for example).
Essentially users copying text from untrusted sources need to be careful.