According to the SVG spec filters can be rendered in either the sRGB or the linearRGB color space, the same goes for gradients and alpha compositing). The latter is controlled by the color-interpolation attribute, the former by the color-interpolation-filters attribute. Inkscape does not handle either of these.
Unfortunately the default for color-interpolation is sRGB, while the default for color-interpolation-filters is linearRGB... This means that Inkscape's rendering of pretty much any filter is incorrect (how severe this is depends on the filter). And perhaps more importantly, it differs from how other renderers behave.
I don't think it's a good idea at this time to truely "solve" this problem. But perhaps we could make sure that new filters created by Inkscape automatically have their color-interpolation-filters attribute set to sRGB? (I have no idea how to do that, so any help is appreciated.)
For reference, I created the following bug report: https://bugs.launchpad.net/inkscape/+bug/365073