I rescued a tortoise that had this same problem. We took her straight to the vet and found out that swelling can be caused by bad diet and environment, which she did have before we got her.
Make sure you are feeding her the right foods, and make sure she also has access to UV light, either sunlight (glass won't let the UVB though so it has to be outside) or a special UV reptile lamp.
I've found that pet shops don't always give the right advice, but the internet is loaded with good information.
Either way a visit to the vet is a good idea, be sure to pick a reptile specialist and be sure to ask for environment and diet advice.
Nov 18, 2010
Tortoise Eye Problems by: Shelly
I'm sorry to tell you that your tortoise does have a serious problem, maybe more than one. The swollen eyes probably mean it has an eye infection. Since tortoises use vision to find food, this is very serious. It will not improve on its own as you have discovered. Please take your tortoise to a vet as soon as possible.
The vet will do an examination and ask you questions that can help with other problems your tortoise may have. For example, there could be diet and lighting problems or any other of a number of things wrong.