Yeah I think a lot of people forget (because it's kinda obscure) that the Emperor's strength and forces are about equal with the combined power of the Landsraad, with the Guild being an ostensibly neutral but very powerful third party. Each of those parties needs the others to survive so for the Emperor to take over military action against a Great House is a huge deal like you said.

In contemporary political terms, it might be like the president sending the Secret Service to murder a Senator or Supreme Court judge.