Prague's concern is not about nuclear going green, but about it not going green enough:

"According to Beneš, new units in Dukovany would be the last new nuclear energy source built in Czechia if the proposal was approved with its current criteria. Investments for the modernisation of existing old units in Dukovany and Temelin would also breach the new taxonomy."

Translation: anti-nuclear forces in the EU are adopting a technique exploited by fossil fuel interests in the U.S.: by forbidding modernization of existing older units they are forcing older units to close while limiting new nuclear to "advanced nuclear" technologies. Then, by progressively raising the bar for what can be considered "advanced", new nuclear can be stalled indefinitely.