I agree with wintertime, instead of incentiviseing "waiting to win", why not build a multipliers for playing more often and playing longer. For example if a unit in the game requires 3 hours to build. I would make either a resource bonuses or build time reduction for returning to the game before that 3 hours.
Or on the topic of the interest rates, instead of keeping a locked interest rate, make it variable interest. If a player, plays for an hour the interest rate maxes out (9.5%) and the more a player is inactive the more the interest rate drops (maybe half every hour of inactivity), that way your players will be encouraged to play more often earning a higher interest rate for playing more and playing more often. You could create interest rate boosters which the player could earn by completing challenges as well, that way players don't feel oppressed by having to log on every 45 mins just to keep their interest rate up. Try to challenge players at least once every time they log on.
Creating build time reductions can be done "in fiction" as well, saying that your factories are "inspired by your presents". This also encourages focused play, separating hardcore players from casual players.
I would only explore interest rates and other banking complications if you're going to build fun game play challenges around them. Banking isn't fun (at least I don't think it is). So if you're going to add banking elements make sure you have a reason to add it and not just to ensure you're player has resources, because their are always way more fun ways of gathering production resources then just waiting for them to accumulate (for example: salvaging ruins, recycling lesser units, completing exploration/gathering/combat/puzzle tasks, etc:)
By the way I like the back story, its a fun fiction and it does draw me in. My only suggestion would be to create a personal layer of story. To connect the player to a handful of individuals. It's challenging, but it separates good RTS from great ones.