The easiest method I know of is to buy a genuine JLINK and use Segger software to read/write Flash. If you only need it for Atmel devices, then SAM-ICE is a cheaper option, as is JLINK-EDU version.
Thanks. In this case, easiest also includes cheap as this is going to be used only once.
I think I found a cheap China alternative: http://www.ebay.com/itm/-/182197178568
It says it supports ARM7TDMI so allegedly it would work, wondering if someone can confirm ?
I think all the cheap "JLINK" adapters on ebay are unofficial clones, Segger call them counterfeit. The Segger software detects clones and refuses to work with them, so I would not advise buying a clone.
The Flash writing algorithms are in the software, so the questions are 1) what software supports SAM7S series, 2) what JTAG adapters does that software support.
So for example, IAR and Keil support SAM7S and a range of adapters, but the free versions of IAR/Keil might be limited to 32K. The cheap route might use OpenOCD, but you might end up having to write your own programming routines, as well as a lot of messing with config files.
I have been down all these routes, so I can tell you the easiest method is an official Segger JLINK. The cheap routes eat up a whole lot of time, and is not easy.
I'm somewhat surprised that basic features such as firmware reading/writing are not able to be done with all JTAG programmers on all chips.
There are many many things that are not standard, so I wouldn't worry about that. If there is no commercial incentive to make products compatible with competitors, it doesn't happen.