I don't own The Well Trained Mind (yet!) so I can't flip through and read the age specific recommendations. I've checked it out from the library twice and read most of it. I like a lot of the ideas. So here's my opinion with that in mind.
If you are talking 4-5 hours (especially all in a row or with only one break) of focused seat work for an active 6 year old boy, yes I think its too much. Is he writing? Is he reading? Here's what I would do.
Writing With Ease Level 1- This should only take about 15-20 minutes a day and I'd probably do lessons 4-5 days a week. He'd be working on good listening skills and summarizing as well as handwriting. The handwriting is minimal. Most of the lesson is oral. There is some grammar to this as well. This is very gentle and short, but my children have been gaining a lot from it.
Sequential Spelling Level 1- If he is already reading and writing I'd recommend starting Spelling. If he isn't I would wait. This Spelling program is also short and sweet. My kids enjoy it. The like to see the word family patterns and get to correct any mistakes themselves immediately which helps retention. I use a big white board and they each use a small whiteboard. Paper is fine too, mine just enjoy using the board and it saves paper. The lessons should take 15-20 minutes. I'd do this 3-5 times a week depending on how much he likes it.
Math- It sounds like you've got something that is working for you so stick with it!
If he isn't reading I'd consider doing The Ordinary Parents Guide to Teaching Reading. If he isn't writing I would still do the Writing With Ease. You could use the copywork to teach him. Or you could do something focused like Handwriting Without Tears. Honestly HWT didn't work for us, copywork did.
Science- lots of nature study and books. My kids enjoyed the Let's Read and Find Out Series. I was able to check these out from the library. Each has several simple, related experiments.
History- I wouldn't worry over this too much. If he's interested do a unit study approach to geography, study one country at a time. Or maybe read him Story of the World or listen to the audio cds. But only so much as is interesting for him.
That and I would read to him as much as he'd like, involve him in chores and cooking, and take him out into the world, nature and everyday errands. Most six year olds have lots of questions. They learn a lot when we take the time to answer them, even if it means we have to research it ourselves. And I wouldn't necessarily do all that at once, but broken up throughout the day as it fit in. Between active play and normal life.