Getting turned down doesn't affect your credit rating as such, but applying for lots of credit does. One or two applications shouldn't make much difference.
And an important point to remember, seeing as you are obviously responsible and careful with your finances, being overdrawn is not a negative on your credit history if it's within your agreed limit. Being in unauthorised overdraft is a negative, so bear this in mind before taking the 'do nothing' option.
Also, when they reduce your o/d to �1000, will you have to pay interest on the �600? If so, it will cost you more than �20 per month.
You might be better off taking their 6% loan and paying what's left of your �250-�300 either off your overdraft (if they charge interest) or into a savings account paying 6% or more (if they don't)