Application.LevelLoad() freezes both the Player and Editor on large scenes

I've noticed a really strange issue in Unity 5.1.2.f1. I have a large scene with a lot of instantiated in runtime GameObjects (mostly disabled). The scene works smoothly (I've written a simple custom "occlusion culling" that enables / disables GameObjects depending on visibility checked with raycasts). But when I want to load another scene via Application.LevelLoad() the Player freezes and crashes, and the Editor freezes completely without a crash. The exact same scene with less objects appears to work just fine. The same scene worked OK on 4.6.7.

I've tried removing all the objects from the scene, before loading a new one, but the result is the same. I've also tried using Application.LevelLoadAsync() and Application.LevelLoadAdditiveAsync(). That doesn't freeze the Editor, but i also doesn't load any scene. No warnings or errors are displayed in the Console.

The bug number I've uploaded is 722749. Unfortunately I couldn't make it public, because of the attached project I'm working on. I will try to replicate this in an "artificial environment" and attach the project.

If someone experienced similar issues or have an idea for a workaround, please share.