The way the specter edition of the record is played - it's quite clear they knew it's not Geth.
The narrative changes from Geth Dreadnought to Unknown Aggressor suspected to be a Reaper and there's the whole slide with data on Sovereign. They also hid the fact that Saren was involved in official version.
It's clearly a cover up.
And they suspected, means they believed. They didn't dismiss that claim in the CLASSIFIED file.