Your request is VERY specific, and as such, very hard to fulfill.
There are no 8-bit game creators, that I know of, especially in a point and click way, and even less for GNU/Linux.
From point and click game creating, you could find eventually what you look for in Flash, and create flash games. That would involve programming of course, but most of the graphical part would be "point and click". About Flash under Linux, however, it's not really easy, you can find some informations on this question from StackOverflow: http://stackoverflow.com/questions/1356077/how-to-write-flash-action-scripts-in-linux-machine.
In general, if you are interested in developing in Flash, then you can find something for the setting of "8-bit-like games" in the flixel engine. This engine is dedicated to the kind of "rendering" you seek, and allows operations on the pixel level. You can find examples on the given link.
I don't know about developing flixel applications, this is only a recommendation, it's up to you to see if it would suit you, and if it would be worth to learn to develop with this framework.
Edit: Note though that this flixel is pure ActionScript, so it would be only programming, unlike a classic flash application. In this case, no "point and click" editing, only code, so it might no suit your needs.