OMG, an 8$ chip when a (looking at your first scope shot) 0.50$ 74ALVC04 powered with 2v (yes, this ICs inputs are 3.6v tolerant even powered with 2v) and 2 diodes will do the same job, though the logic switch edge will be fixed at ~1v on each input. Powering your IO bank at 3.3v would mean no ICs needed, just the 1-2 silicon diodes to separate the 2 voltage levels to 2 different inputs.
Ok, back to your question:
For CycloneIV, you have 0.3-0.5v above the VCCIO before the clamping diodes engage.
An output resistor divider would work with your illustrated circuit.
A 1k series resistor alone would also work so long as the selected IO pin has the PCI clamp diodes mentioned in the CycloneIV hand book in section 3, DC electrical characteristics.
As for powering an IO bank with 3.3v and telling quartus to run the IOs in differential 2.5vLVDS, I don't think it will destroy the chip, however, I never done this.
Can you change your dev board's 3.3v regulator to 2.5v?
Most other 3.3v lvcmos ICs should work at 2.5v, but a bit slower.