Which end up with McLaren refusing to sell a bigger share, Mercedes buying Brawn, selling their share and McLaren switching engine supplier.
Mercedes wanted their own team, McLaren weren't prepared to sell a majority share to them, probably based on the fact that manufacturers can easily come and go in F1 and that wouldn't secure the future of McLaren. Also consider the formation of McLaren Automotive as motivation to keep the team an independant outfit.
McLaren switching to Honda again isn't a sign of a bad relationship with Mercedes, it's just that Honda can offer them a partnership similar to what they had with Merc that is now not possible with Merc having a works team on the grid.
Some people are too quick to read too much into things like this, without considering how customer engine relationships work anyway. McLaren will get exactly the same treatment as Williams and Force India. That is less than what they have enjoyed before, but it is still professional and supportive. The thing with customer teams is that if they want to they can buy the contract out at any time and go to someone else, taking all that information with them to the new supplier. That's exactly the same scenario as with McLaren going to Honda, only it's been a done deal much earlier than other changes in supplier have gone traditionally.
Consider the Toro Rosso deal with Renault. That was only announced in May last year, so presumably before that was arranged they were working at least in preliminary stages with Ferrari on their 2014 design program. Moving to Renault would mean all that precious information being transferred over, because you can't unlearn something no matter how small or opaque the information is. Ferrari as a customer engine provider know that this scenario is possible with customer teams so they restrict what they share with the team to just the essentials (still probably a large % of the total knowledge of the package), and to make sure there are no issues it's all nice and contractual, so both parties have something written down if one or other doesn't fulfill their end.