"whom" is wrong in 3 different ways in my opinion:
(1) It should be "who", not "whom". I find that hypercorrection immensely annoying.
(2) But actually, since Lily is a company, it should be "which", not "who".
(3) But even "which despite raising […] has filed" is wrong. It actually should just be "Lily, despite raising […], has filed" or "Lily, which raised […], has filed". "which despite raising" subordinates "has filed […]", so the whole sentence turns into a noun phrase missing its verb phrase.
Point 2 to me was not about singular/plural, but about companies being animate/inanimate. It turns out that there used to be a very clear preference for "which", but by now, "who" is winning out in US usage: https://books.google.com/ngrams/graph?content=company+which%...
Always treating organisations as singular rather than plural ("has" vs "have") is something specific to American English, and treating them as plural isn't ungrammatical in English.