EDIT: Jeff Blair reports that it's 2 years at $1.9 million/year.
The move certainly gives the perception that the Jays will look for McDonald to be the regular SS next season. But he's not making so much that it would prevent the Jays from making another move and using McDonald as a utility infielder / defensive replacement / pinch runner if the opportunity arose. The free agent market is thin and if a team has a good young SS prospect they're not likely to give him up easily.
Signing McDonald for 2 years seems a bit unnecessary. Are there teams out there that are going to sign McDonald for 2 years and/or give him a better oppurtunity than the Jays will? I can't image that there are. Is McDonald so good that the Jays should want to sign him for 2 years? No. He's 33 in a couple weeks and at that age you generally only get worse.