well filtering a texture atlas is always going to give you issues like you describe, keeping a transparent border around sub-textures is the usual generic solution, GL_CLAMP_TO_EDGE won't help you as you're not necessarily addressing the texture up to it's edge for all sub-images.
Caveats you must accept for the performance gains of a texture atlas.
I'm working in OpenGL 4.x currently and I don't support anything less than 3. I did that specifically because I didn't have to jump through all the hoops. I'm guaranteed to have NPOT support, guaranteed to have uniform buffers, tessellation stages on 4.x hardware blah blah blah
it's so much less of a headache than GL1.x GL2.x, GLES etc
And it's only a matter of time before GL2.x is about as common as Glide (3DFX) plus the next itteration of GLES will be in the GL3.x/4.x style.
If you're working on projects with epic timescales, you've got to plan 3/4 years ahead. If you don't then you end up like GLScene with almost no ability to switch to the current versions (GL3 is old now) except a significant re-write of many parts.
I mean look at all those epic game titles from the 90s, games coming out in 1997/98 that ran in DOS!
You've got to think ahead, I'd advise anybody to throw GL1.x and 2.X out of the window immediately (pun intended) and work in a GL3 core profile at the very least. Doesn't matter if your card doesn't support it, that's what Mesa is for. And if you miss immediate mode functions for debugging purpouses, use a delphi/lazarus form with your window to display stuff or just re-implement immediate mode functionality on top of VBOs and shaders, I did that and never looked back.
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