Yes, you can file as a resident alien in 2024 and claim the Standard Deduction. There's no provision, though for not claiming your refund unless you are trying to make amends for the past. If this is the case, the only way you can make amends is by amending your previous tax returns as PK mentions.
In your second question, you can file separately or jointly if you wish to be treated as resident aliens for tax reporting purposes. If this is the case, then Married Filing Jointly would give you a much better tax return. There is no advantage to File separately in this case.
If you wish to amend your prior year's tax returns, you would need to contact Sprint Tax here. TurboTax does not prepare or amend 1040 NR returns.
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