I think it's a stretch to say that the EU is "encouraging" such scummy practices. It's likely that they just collated a list of all software used widely by government departments within the EU -- and thus FileZilla is on the list. Ultimately, a potential 0day causing RCE within a government department is more of a concern to the EU than the optional malware you get during FileZilla's installation.
I haven't used Filezilla in a _long_ time -- is the malware optional? I imagine that most EU governments image their machines, so they IT departments likely aren't installing the malware.
And there is also the consideration that governments will continue to use Filezilla even if there isn't EU funding to make it more secure -- malware and all.
Seems kind of bizarre the EU would encourage such practises.