Partnering with Pixar just makes good sense. Even if 10 years ago Disney were cutting edge CGI and turning out great flicks, if Steve Jobs were to come to you and say "this is what we can do for you, this is what your percentage of the take will be and all it will cost is X" , wouldn't you jump on the deal ?
Really, no.
If you can produce better core product for yourself than a vendor can, and quality is an integral part of your product, then you do it yourself, unless you simply cannot afford the investment.
Clearly Disney could afford the investment, they just chose to invest in other things.
In the hypothetical world where Disney still produced product of at least equal quality to their vendor, it might not have too many negative long term repercussions. But in the real world, where Disney is a distant second, its become a serious problem.
Also looking at things realistically, I think the reasons for going with Pixar, and the reasons for Disney's internal animation struggles are largely the same. In other words, while it might be hypothetically possible for them to produce top quality work while also buying it from Pixar, I don't think there was a chance in heck of it happening.
So now where are they?
-Faced with likely becoming the #2 animation studio in name, as well as in substance. For a company that relies so much on its brand value, this could be HUGE in the future.
-Faced with signing new agreements with unknown vendors.
-Faced with building it internally anyway.