If Thoreau could feel that his night in jail was time well spent, then he certainly could have felt that his time at Walden Pond was well spent.  In his "Conclusion," Walden writes that he left the woods "for as good a reason as I went there.  He wanted to live deliberately and not fall into a "particular route and make a beaten path for myself."  That he felt satisfied and better for the experience is conveyed in these words of Thoreau:

I learned this, at least, by my experiment:  That is one advances confidently in the direction of his dreams, and endeavors to live the life which he has imagined, he will meet with a success unexpected in common hours.

I sense that there is little disconnect between Thoreau's writing and philosophy and his beliefs as to satisfaction.  I think that the Conclusion to Walden would prove this.  He sincerely believes that in embracing the life of solitude and inward reflection that he has advocated, human life and consciousness can be more worthwhile and meaningful:

Be a Columbus to whole new continents and worlds within you, opening new channels, not of trade, but of thought.

I don't think that he suggests this unless he sincerely believes it.  In this, I think that Walden would say that his time was well spent for it was spent doing what he thought appropriate and activating his own sense of freedom as opposed to allowing other forces to dictate his actions.  It would be in this where I think that Thoreau would find meaning in what he feels and advocates in his writing.