Even if you're buried in the D-zone, 39% is still particularly awful. 40% shot attempts/scoring chances is like the Mendoza line. If you can't crack that, you shouldn't be in the NHL.
Back in the heyday, an uber-defensively deployed Malhotra was 45+%. During the Blackhawks runs, Kruger (who had probably the worst zone start ratio of any regular NHLer) was around 50% IIRC. I'm not a Sutter fan by any stretch, but he had worse zone deployment (and tougher competition) yet was still 44/45% in corsi and xGoals. If you scroll through the lists of forwards with the toughest zone start ratios last year, Beagle is actually uniquely bad. Like, Faksa and Sissons were cracking 50% in tough deployment.
So yes, in sum, Beagle is not very good. And bringing him on in an effort to "teach" defense to Petterson is extremely foolish rationale.