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In your case, probably, only manually draw with simple primitives (rectangles, lines) on the DrawingArea using DrawingMethods (this is under gtk2, but under the 3rd it will be similar). It is unlikely that somewhere there is a SPECIAL library for drawing EXACTLY histograms EXACTLY under GTK3, moreover, it is lightweight enough for you.
If there are no TECHNICAL limitations preventing you from using matplotlib, then you will probably end up using it. All python software under GTK that can draw histograms is one way or another based on matplotlib. There don't seem to be any real alternatives.
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