I think some are blending the responsibility of ATC and the pilot here.
From an ATC point of view, it's pretty clear... according to DOC 4444 item 4.10.3.2 note 3:
"The objectives of the air traffic control service as prescribed in Annex 11 do not include prevention of collision with terrain. The procedures prescribed in this document do not relieve pilots of their responsibility to ensure that any clearances issued by air traffic control units are safe in this respect."
And item 4.10.3.1
"Except when specifically authorized by the appropriate authority, cruising levels below the minimum flight altitudes established by the State shall not be assigned."
According to this, ATC give an IFR clearance at the lowest available (safe) level, how the pilot gets there, from below the MSA, IFR or VFR, that one is on the pilot, not ATC.
As a pilot myself, if caught below MSA and have to go IFR, I'd look at my chart, point my aircraft in a safe direction, and use best rate of climb to get up to the MSA.... I really cannot see any other way of doing it...