Yes, that's alliteration. Yes, you should consider changing it.
Why doesn't your thunderstorm serve a function? Every word needs to either support the theme, reveal character, or advance the plot.
If your subconscious is trying to support the theme with this storm, look to see where else that theme might trying to break through.
The theme of the book revolves around the excesses of the Nazi regime, so I suppose there's a gloomy, stormy feel to the whole thing. Not sure what you mean about the theme trying to break through... Or what I should do about it if I did locate these occurrences.
Why should I change the unintentional alliteration? What harm is it doing?