Large bases a more expensive to run, by how much I don't know, it depends on how many aircraft are based there. Best thing to do is keep bases at the maximum size you need them to be at any time and upgrade when you need to. With downgrading it's probably best to work out the difference in the staff/office costs that I believe the game gives you between your current size and downgraded size.
Let's say the difference is 10k per month and you have costs of 400k, after 40 months (3 and a bit years) you will have broken even on the savings made to the initial investment you made to downgrade. So you will save money over a period longer that 40 months. If you plan on reintroducing a large aircraft within about 10 years think about it carefully because you will have both the downgrade cost and upgrade costs to bear, so that probably won't work out to the financial benefit of your airline.
To sum up, possibly worth it if you are going to stick to medium aircraft there for a long period, but if you aren't, it may well be worth keeping the status quo. Go do some sums!