I thought the EA was a militaristic, expansionist type of government. And that they developed the Punisher cannon to bombard worlds with. You seem to start from the premise that the Icanus/Punisher Cannon is a defensive weapon. I think it's geared with offense in mind. Think: a planetary-bombardment beam would be one hell of an incentive to submit to the EA. Of course, factor in the problem that such a big cannon isn't very portable... probably couldn't move it at all on its own. So: the Icanus project makes more sense in that all it really is a Punisher-cannon transport that they decided to turn into a warship of its own.
We will probably find out if the EA are expansionist and militaristic type of government in INFA2, but from what we know right now, from INFA1 and INFR1 (and the storyline of course of INF SCP), we can tell that they are an aggressive society. I admit that I did have some oversight in that perspective. However, the men who had approved the Icanus in the first place probably calculated how long it would take, and not even thinking about what would happen if there was sabotage. They probably calculated that it would be finished after the civil war, and however wins, the Icanus probably won't be used anyway. So that leaves the Icanus as a foolish choice, I personally wouldn't choose to have the Icanus commissioned. But perhaps they were preparing for the future when the GTVA would return to Sol.
You can tell from Darius' Icanus Fiction (non-canon, of course) and from Aldo's modeldump (where I believe it was recovered) that the Icanus and Punisher were originally separate designs. This probably supports your theory that the Icanus was an offensive weapon designed to carry the Punisher, or that the Punisher was originally a massive RBC (yeah, massive) that was integrated into the Icanus' design.
Also: time-constraints. Even if they didn't start until later than 2335 to begin construction (who knows? Maybe construction could have begun while the Great War was going on?), the way the story of the Icanus tells it, it sounds as though the Punisher was already built or close-to-being-built when Project Icanus was approved. That's at least a third of the construction time done right there. Furthermore: since the EA didn't sortie the Icanus during the EA-GTVA war in 2401, I think it safe to assume that it wasn't built by that point. In order to fight the Gigas later on, it would of course have been extremely close to being built, but not quite functional.
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NO INFA SPOILERS PLEASE</snip>
It is also impossible the Icanus was created during the Great War or INFA because that would make the Icanus a Martian design (it is also clearly stated the Atlantis station was above Mars), which it wasn't. If it was a Martian design, the Earthers would have probably attempted an attack on the shipyards. Another pointer is the the Icanus uses EA textures rather than the INFA Fenris-style textures. So that would probably mean the Icanus was conceived after INFA, but parts of it were already constructed, or judging from Darius' Icanus fiction, after the formation of the EA, but that isn't INF canon so it's nothing to really go by.
And the 66 years thing was also unrealistic. The Colossus was only 1327 by 2204 by 6117, while the Icanus was 7109 by 5061 by 19367. That's already approximately six times wider, more than twice as high and three times longer than the Colossus.