Can you specify which books you're referring to? I have yet to see a mention of taking such a long time in clearing a vessel.
As for destroying it, you don't need to destroy it, merely make it incapable of retaliation. In the case of the Battleship Bismarck, they first crippled her ability to run, then pounded her into scrap, unable to return fire. Only then did they sink her.
All you would really have to do is use an ion cannon to keep it from being able to fire, then pour the troops in. Yes it would take the equivalent of urban warfare to subdue the crew, but weeks? Unlikely. One team grabbing the fusion plant would force their surrender because without power, the ship is dead in all purposes, or could be destroyed by setting it to overload.
I think what the problem is can be described as amateurs looking at situation, and going from there bythely ignorant of the size of the problem. I noticed it when they went to war with only 2.1 million clones. Using them as shock troops makes sense, but that is the type of combat that chews up formations and reduces them to uselessness. As John Ringo in Von Neuman's War pointed out, you pour them onto the beach, and plan for some or hopefully most to survive long enough to succeed in their mission but not to come home. Planning the D Day, Eisenhower anticipated 20K casualties before it would become difficult to continue (Entire ground force commited, 175K). The 10,000 they did lose was small change in comparison.