The modification is to the default configuration of all the full nodes on the network. If you downgrade to send a "non-standard" transaction, you may find that all of your connected peers will refuse to relay the transaction and the few miners that you happen to connect directly to will refuse to add it to a block. If may take a VERY long time for a generous miner to hear about the transaction and choose to add it to a block for you and then you have to hope that miner has enough hash power to actually solve a block in your lifetime.
It is possible that many peers and/or miners will choose to remove the restriction and relay/confirm these "non-standard" transactions, but be aware that you are taking a risk. Do you have a plan on how you will handle the situation if your transaction still doesn't have its first confirmation after 3 months?
I forgot that the change was a node change instead of a blockchain change, so the software change won't work. You are correct. Just wait till you have a bigger output to send to everyone, or attach a very high TX fee.