Hi roroba,
Yours is a very tricky question because it depends highly on the number of samples you will be processing. The 3130 is a much more expensive instrument, but if you will be running hundreds of samples then you simply have to use a 3130. On the other hand if you will only be running a few samples at a time, then the 310 is the more appropriate instrument. At laboratories I have worked at that performed these types of experiments we had both instruments and used them depending on the number of samples that needed to be processed.
Beyond the costs of the instruments themselves you need to determine what volume reactions you will, and can, run with your instruments. The lower the reaction volume you can reproducibly run the cheaper it will be.
Unfortunately I do not have a simple answer to your question since the number of variables you need to calculate, and the capabilities you need to identify, are simply too many to be able to simply say, or compare, the costs of these two different instrument.
My recommendation to you is to sit down on a computer, open an Excel spreadsheet, and start working out the costs.
Good luck