だから indicates the cause/reason as in your initial translation and そう refers to デュエル・マスターズは遊☆戯☆王のパクリだ, thus, 本当にそうだから means "because it is really so (= because Duel Masters is really a rip-off of Yu-Gi-Oh!)".
I know it can act as a softener at the end of a sentence so I'm tempted to split it in two; "デュエル・マスターズは遊☆戯☆王のパクリっぽいけど" and "本当にそうだから困っちゃうね" respectively.
(couldn't edit my previous post due to 15 min limit)
So would the overall sentence be something like "Duel Masters is a rip-off of Yu-Gi-Oh!, but it's (just) embarrassing/annoying because it is really so. What should they do? Stop copying!"?
If those are a conversation among three people, which is my current interpretation, the subject of した is "we". Or, the most convenient way might be to avoid denoting who the subject who should do is, just like the original Japanese sentence, for instance, "How should it be treated?".
Because it's curiously similar to a "coded" message in a game except with the two names replaced, so either the person writing this was riffing off the original or you've taken the time to replace the game names for some weird reason.
I googled and found this site before posting my initial reply. It seems that the sentence is appeared in an anime, which is written in code/alphabet called デジ文字.
EDIT:
Oops, I didn't realize it's actually デジモンはポケモンの in the site I linked, not デュエル・マスターズは遊☆戯☆王の. So, nekojita-san might refer to this sentence, too?