Remove the auto-sell option from gates but still allow manual depositing of minerals.
Implement a LCDVM (Luminescent Crystal Distributing and Vending Machine).
This vending machine will have an auto-sell option and will act as a mineral proxy.
Players can deposit their minerals into the machine and get their 5 crowns per mineral.
Players can then pay to have the minerals transferred from this machine to the gate and stratum of their choice. (1 crown ea for current stratum, 2 crowns for current + 1, 3 crowns for current + 2 etc).
Have regular mineral dumps into the left-most gate to prevent 'stagnant' minerals. (once per day, once every two days, once a week, up to you). If there are more minerals in the LCDVM than is required to finish the gate then the excess gets deposited to the next gate and so on.
This way, players who don't care about crafting gates get their crowns and don't interfere with players that do.
Players can still boost gates if they want to.
Players can still organise community gate crafting initiatives on forums/in-game because players can still deposit into gates manually.
Edit: http://forums.spiralknights.com/en/node/8005
Just realised someone already beat me to it but mine's a little bit different.
This looks similar to my suggestion here, though it has some very interesting differences.
One issue I see is that regular automatic mineral dumps would mean that the minerals from people who don't care about gates would still dwarf the intentionally-deposited ones, unless I'm misunderstanding what you mean there. If the dump is less frequent than the gate launches, then it wouldn't affect all gates, but it would have a proportionately larger impact when it does dump.
I would guess the transfer cost should be higher than 1 crown, as that makes every crown I get effectively a mineral of my choice — which makes manual mineral gathering pretty pointless for the purpose of gate influence. In fact, the handful of crowns I get from minerals would give me five times the influence of the minerals I manually deposited! Such a system might work fine, and it would provide a major crown sink, but it would change the gate crafting system more than it first appears. The transfer cost would have to be tweaked to balance how effective transferring is relative to manual mineral collection.
How would this interact with boosts? The LCDVM couldn't provide less payout than manual depositing, or people would manually deposit even if they don't care about construction. It wouldn't work to give people the boosted price without actually sending the minerals to the boosted gates, as the boost wouldn't affect gate construction then.
My best suggestion at this point is to make boosts more granular, combine them with transfers, and have the LCDVM only store unboosted minerals. Rather than permanently boosting a depth for a high price or manually transferring from the LCDVM, I could put any amount of crowns down as a "bounty" for a particular depth. If there are stored minerals, it would act as a transfer and immediately pull them out of storage. If there aren't, it would stay around as a boost for future mineral deposits — whether manually deposited or automatic — until it's depleted.
How this plays out depends on how much it costs to "buy" a mineral, since that determines if supply or demand for stored minerals is higher. If the transfer/boost cost is high enough that minerals stockpile, then supply is higher and every bounty would be a transfer from the LCDVM. If there's more than enough bounties to cover the minerals coming in, then it's a more flexible boost system and the LCDVM basically becomes like my quick-sell station as it would never store minerals.