Heat your grill to medium-high heat , or a large heavy skillet.
Add the brats, and cook until browned on all sides, about 5 minutes (doesn't need to be cooked completely through...they will finish cooking while braising). Set aside.
In a Dutch oven (or large sturdy pot), over medium eat, warm the olive oil.
Add the onion and saute until tender and golden, about 10 minutes.
Add the flour and cook, stirring for another minute.
Whisk in the ale and cider until the mixture is smooth and bubbly.
Add the thyme and stock, whisking to blend, and bring to a simmer.
Return the sausages to the pot and cover.
Reduce the heat to medium-low, and cook for 15 minutes.
Uncover, add the sauerkraut, and simmer until the sauce is slightly reduced, about 5 minutes longer.
Taste and season with salt and pepper.
Divide the sausages and sauce among serving bowls and serve at once.