They were plenty happy with it when BTC was crashing. People just like to whine. Converting to JPY in MtGox's case and USD in Bitfinex's case was the reasonable thing to do. Denominating massive debts in cryptocurrency is an insane thing in a market this young and volatile.
I don't think this was terribly good for them when bitcoin was crashing either, because it still ate into the amount they'd get paid out since the underlying assets were still partially in bitcoins. The bankruptcy trustee basically gave Mark Karpeles free options on bitcoin with all the customers he'd screwed over as forced counterparties.
