But having seen England beat Australia 4-1 in an ODI series Down Under earlier this year, captain Morgan was confident this loss would not do lasting damage to England's morale.
England were all out for 365 after Scotland made 371 for five, their highest total in a one-day worldwide.
"I'm really confident, feel like I'm bowling quite nicely especially with the white ball", he said.
England arguably plumbed new depths at the last World Cup when they exited in the group stages with barely a whimper.
The ICC has reduced the number of teams at the 2019 World Cup to 10 from 14, making it far more hard for associate nations to qualify.
The world No 1 one-day worldwide side were embarrassed in Edinburgh but, ahead of a series against Australia which starts on Wednesday, Morgan chose to view it as valuable preparation. The partnership between M Cross and K Coetzer was the joint fourth highest opening partnership in ODIs for Scotland.
He will be up against Jonny Bairstow who is enjoying a rich vein of form and will be taking guard in the match after scoring three successive hundreds in this format.
Scotland captain Kyle Coetzer said: "It was an outstanding game and the guys did unbelievably well to knock over the top side in the world".
But they lost both openers in quick succession to be 107 for two.
Less than a year remains until England look to add a first piece of 50-over silverware to their trophy cabinet, with few better chances of ending their barren run than a tournament on home soil.
Jason Roy and Bairstow launched England's reply with a century stand but Bairstow holed out when he might have won the game. But Bairstow was caught on 105, then a stupid mistake by Alex Hales saw England's Joe Root run out for just 29 with England on 220.
Ali's 46 threatened to spare England's blushes only for the all-rounder to be undone by a slower delivery from left-arm spinner Mark Watt.
The Oval will be just Agar's fifth ODI since he made his debut against England at Old Trafford in 2015 - although English audiences are more likely to remember him for his 98 on Test debut batting at No. 11 in the 2013 Ashes - and he now feels a more rounded cricketer.