An alternative suggestion:
When your funds are negative, the timeframe is locked at 5s and cannot be set to anything faster. This would be the only penalty for having negative funds.
This makes it easy for the player to sell stuff from any base (including base facilities), and even gives them a chance to raid any existing wrecks or the like if they have some easy way to raid stuff for cash.
The only problem, I guess, is that someone who has completely lost the game due to lack of funds might be tempted to try and continue at 5s, since it might not be clear that you're not supposed to do that. (And that the appropriate response if you can't scrounge up the funds is to give up.) Maybe replace the faster time buttons with a "give up" button or something.