Wellington students are probably advantaged when it comes to applying for a first year job in Wellington, but it's definitely still achievable to get a job if you didn't do your clinical years there. Each year Wellington seems to hire a few people from outside of Wellington. At the same time, each year students based in Wellington miss out on getting a job in Wellington.
The RMO recruiters at Wellington say the main thing they look for is people who have good reasons for wanting a job there (after all, they only want to hire people who really want the job). For example, people with strong family reasons tend to be ranked higher. They also favour people who have done TI in Wellington, done a placement in Wellington, or who have visited/made contact in advance. Most DHBs are like this. Obviously your CV and references also count for something, but from what the recruiters claim, they aren't the most important factors.
So, I think the main things to consider are:
1 - Doing clinical years at Wellington could increase your chances of getting a job there (provided you impress the right people). However, Wellington jobs are competitive, and you may still miss out.
2 - You can still get a job if you don't do clinical years in Wellington, particularly if you do the right things to impress the recruiters and have good reasons for wanting Wellington.
3 - You don't stop moving around the country after graduation. As a registrar you may be expected to work in a number of different hospitals. Even if you start work in Wellington straight after graduation you could be moving town in a couple of years. Similarly, even if you don't start in Wellington you may end up working there in a couple of years anyway.
4 - There's a good chance that, after 3 years in Christchurch, you'll want to stay there to work. It's happened to plenty of people before!
I think that if you want Christchurch for clinical years, go for Christchurch.