Agreed, it made the crew look extremely incompetent. In reality, those 2 ferengi shouldn't have had a prayer of a chance against a fully manned starship.
The worst thing is that all Janeway would have had to do after she beamed them up and listening to that plea of Arridor: 'Nice try, mr. Arridor, but I won't have any of it. I don't buy that removing you would cause more damage than your arrival already did. You'll be confined while we travel through the wormhole and after that as well, until we get an opportunity to ship you off to Ferenginar. Mr Tuvok, will you escort them to the brig?'.