Why do you want to open the files in Illustrator?
You can export PDF from ID, and choose "crop image data to frame" in the export options (I don't know if this is availble in .eps export because I never export a page as .eps).
There is probably nothing you can do to prevent your printer from "messing around" with your file if he's intent on doing so and has the right software. Perhaps you should be looking for a printer you can trust.
Thanks. I agree about a trustworthy printer but in this case it's out of my hand. EPS is a legacy and request from the printer who prefer non compressed artwork file. The file is huge but the image will be good.
On behalf of Adobe Systems Incorporated ...
Adobe Illustrator is not, repeat is not, repeat yet again is not a general purpose EPS file editor. The only EPS files that Adobe Illlustrator can fully and properly edit are EPS files saved directly by the version of Adobe Illustrator you are opening the EPS file with (or later Illustrator versions). EPS files saved from Adobe InDesign do not so-qualify.
If you open an InDesign-exported EPS file in Adobe Illustrator, although a "best effort" is made to properly interpret same, certain problems are likely such as changes in color spaces and colors (Illustrator only supports either CMYK or RGB in a .AI, .PDF, or .EPS file being opened; EPS files exported from InDesign are often in multiple color spaces.
Similar comments apply to trying to use Adobe Illustrator as a general purpose PDF editor; it isn't one.
Adobe considers any workflows that include routine opening of non-Illustrator generated EPS (or PDF) files in Adobe Illustrator as highly unreliable and exceptionally poor workflow practice!!!!