I agree that it is a red flag that the CTO on one hand admits that the co-founder is valuable in the 3-6 months it takes to raise a round, and on the other hand asks him to leave after fundraising. At the very least this seems to indicate that the co-founder is essential for fundraising.
I want to stress that you as a co-founder should never let anyone talk you into staying with the company through fundraising and then leave. Telling an investor that a co-founder is leaving just after fundraising does not instill confidence, and planning to leave without telling prospective investors violates their trust. If you do this then you'll get a bad reputation with investors and it quite honestly makes you look like a bad person, so don't ever do that. If the cap-table needs to be redistributed and fixed up do the cleanup before the prospective in-laws come over (investors), as this kind of mess benefits no-one.
I want to stress that you as a co-founder should never let anyone talk you into staying with the company through fundraising and then leave. Telling an investor that a co-founder is leaving just after fundraising does not instill confidence, and planning to leave without telling prospective investors violates their trust. If you do this then you'll get a bad reputation with investors and it quite honestly makes you look like a bad person, so don't ever do that. If the cap-table needs to be redistributed and fixed up do the cleanup before the prospective in-laws come over (investors), as this kind of mess benefits no-one.