Tim.
I am not trying to be rude or put you down, but I don't think it's honesty, I think it's stupidity. If your conscience won't let you charge for the whole room, lower your price slightly and measure the whole room. Keep your measurements on file so you never have to re-measure.
Every time they get a new piece of furniture you won't have to give another estimate, it's a waste of time any other way.
If I run into it where I have 3 bedrooms that don't have much actual exposed carpet, I measure them up, and then subtract one room, tell them I'm giving it to them for free.
Let them know time is money, and you will discount for empty rooms that save you time, but if YOU spend more money cleaning a full room, why should you discount for it? Discount when they save you money. Also, write in a little policy about moving furniture, give them 2 pieces on a smaller house, and anything over 1200 sq. ft. give them four pieces. What if they have just one or two more pieces? "Well, I'm only supposed to move 2 pieces, but I'm not an ogre, OF COURSE I'll move those extra pieces for you."
You will be getting paid enough on your jobs to be the hero, to give them things for free. Why are giving them free stuff? Because you're a nice guy. They want to get their carpets cleaned by a nice guy like you, they'll call you year after year.
Instead of measuring up tiny parts all over the house, you just measure it, and make up for it in free areas. Give them their closets and a bedroom for free, and move that one or two pieces of furniture they just have to have moved, and you'll do fine. They'll be happy, and your job averages will go up. Not to mention, it is a lot easier to raise your prices when you need to raise your prices by just not giving a freebie next time.