I've siliconed small glass brackets in my sump (for float valves and whatnot) and had it back in action within 20 minutes without any problems before. This was with All-Glass brand silicone however, so I know it is aquarium safe.
I think you may have used a silicone that contained either anti-bacterial or anti-mildew agents which is quite toxic to your tank. Carbon, water changes and heavy skimming are all you can really do for your tank now. IIRC Gunjustsuu (sp?) had a similar problem in his tank a while back.
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