Mark-and-Sweep garbage collection need to work over the graph of all objects in the process.
It does not! Generational GC works over the graph of all objects in a generation. Objects that survive one generation are promoted to the next, which is GC'd less often. You therefore get fast reclamation of short-lived temporaries, and infrequent scans of long-lived objects.
and would stall threads to make the operation safe with regard to threads
There are clever things you can do to avoid stop-the-world collections, but generally we just live with the tax.
I can think of no way to work around this and make it efficient.
"Efficiency" is work done divided by cost, so before you spend a lot of time thinking about ways to improve efficiency, start by defining what your metrics are for "work" and "cost".
Mark-and-sweep GCs are efficient enough for the vast majority of business processes; in cases where collection stalls are frequent enough to exceed user-focused performance budgets, my usual advice is to start by reducing collection pressure via pooling or other strategies. We did a lot of that when building the Roslyn C# compiler.
But how are some system/application-programming languages solving it?
I once asked a gardener at Oxford how they got their lawn so nice. "Rake the dew off every morning, mow it once a week, run a lawn roller over it once a month, for 400 years". You too can have a great lawn; start today.
The .NET GC is one of the most heavily tuned pieces of software on the planet. Patrick Dussud did a great job in the initial performance tuning and there has been literally two decades of a team of experts continuing to tweak it.
You solve this performance problem the same way you solve all foundational subsystem performance problems. (1) think about performance of foundational subsystems up front, during design, (2) hire industry leading experts (3) measure measure measure measure measure.... (4) make careful changes designed to achieve particular goals, (5) go back to step 3. Do that for 20 years and you too will have a great GC.