1000 is a little high to waive fees. I would read the fine print, it maybe the type of savings account you have. I usually see $100 minimum balance, or automatic transfer to savings once a month or a checking/savings combo to avoid a monthly fee.
I had a similar issue with a different CU that decided they wanted a min of $250 in the share account or it's $2.50/mo for the low balance.
If I had to put down $1K to avoid $5/mo I would just get a different card. I earn 2.5% APY on my current CU Checking account so..... .01%-.1% isn't going to work for a $1K deposit.
All credit unions require you to have a share savings account; it's your share of the credit union. None of my CUs require a minimum for the savings. For a checking account, there are miniums to avoid fees. It isn't right since you already paid to join the credit union, and they're supposed to be doing things in the best interest of the members. Since it's your oldest account, I would think about the benefits of keeping the card. Like how often you use the card, the benefits of the card (utilization, rewards), and if you have cards that already serve the same purpose.
For the $1000 secure savings loan, it would depend on what you want. If you want a installment loan, then go ahead and deposit the money and get the loan. If you're only doing it to keep the account, think long and hard about the decision. Most CUs don't have a high APY. You could get a better return on that $1000 by opening a bank account and getting a bonus or getting a high yield savings account from a CU.
Which credit union is it? I agree it seems odd that they'd be charging you for having a basic (share savings) account with them. Do you have any significant amount deposited with them in shares, or was it just basically the minimum and your credit card?