* Congo's army routed rebels with U.N. force backing
* Rebel commander fled to Uganda where deal to be signed
* Peace accord will not necessarily bring lasting calm
By Elias Biryabarema and Richard Lough
KAMPALA, Nov 11 (Reuters) - Congo and defeated M23 rebels are to sign a peace deal on Monday aimed at ending the country's most serious conflict in a decade, though other militias still roam and stability remains a distant prospect.
The rebels gave up their 20-month revolt last week after the Democratic Republic of Congo's army, backed by a United Nations force, routed them from their last remaining hilltop hideouts along the border with Rwanda and Uganda.
The peace deal is due to be signed in Entebbe outside the Ugandan capital, Kampala, at around 6 p.m. (1500 GMT).
M23's rebellion had at times risked sucking Congo's neighbours into a wider conflict. United Nations experts documented evidence that Rwanda and Uganda had supported the rebels, straining relations with Kinshasa. Both Kigali and Kampala repeatedly denied the allegations.
The accord will address issues such as amnesty - for the act of rebellion, though not for crimes against humanity - and also allows reintegration of vetted rebels into the army.
"We have said it should be a document that focuses on ending the rebellion, not settling all the problems between Congo, Rwanda and Uganda," one senior diplomat said.
"For acts of rebellion, the DRC government is ready to offer amnesty. But there is no amnesty for major war crimes."
That will almost certainly mean no amnesty for the M23's military commander, Sultani Makenga, who fled across the border and is now being held in Uganda, which has been trying with international support to mediate an end to the fighting.
Makenga's surrender is a big win for Congo as it struggles to impose order and a vindication for the world powers which backed a U.N. intervention brigade with a robust mandate.
But analysts are sceptical there will be sustained peace in a region devastated by two decades of conflict that has killed millions and left millions more destitute despite underground deposits of gold, diamonds and other valuable minerals.
"I don't think there is a track record in the DRC of these sort of issues being resolved," said Brian Dlamini, a country risk analyst for Rand Merchant Bank in South Africa.
"The DRC is a country of many countries," he said.
Kinshasa has limited ability to exert its authority over one of Africa's biggest nations. There is no tarmac road connecting the capital to the main eastern town of Goma.
Deep-seated regional rivalries could still unsettle any shaky peace.
"VITAL FOR RWANDA"
U.N. experts, the United States and others accused Rwanda of backing the M23, despite Kigali's vigorous denials. Aid cuts and diplomatic pressure were seen reasons why Rwanda may have backed off from trying to rescue the M23 when the U.N.-backed Congolese army closed in, analysts say.
But a regional diplomat, in remarks widely echoed, said neighbouring Rwanda would not easily abandon interests in east Congo, which it says is still a haven for Hutu rebels behind Rwanda's 1994 genocide that killed Tutsis and moderate Hutus.
"It's just vital for Rwanda to have influence there. If not with Makenga then with someone else," the diplomat said, although he said the costs of backing M23 had become too high.
At the United Nations in New York, diplomats have indicated that the U.N. force MONUSCO will now help Congo's army against other armed groups, especially the Rwandan Hutu FDLR rebels.
"I think the FDLR are very clearly understanding that either they surrender or there will be armed action against them," Mary Robinson, the U.N. special envoy to the Great Lakes region, told Reuters in the Ethiopian capital on Sunday.
"That is a new reality for them to face," she said.
She said some other smaller armed groups had already indicated to MONUSCO that they were now ready to make peace.
"The hope is that if you eliminate the larger groups, the others will see the writing on the wall," U.S. special envoy to the Great Lakes, Russ Feingold, said in South Africa last week.
He said an "appropriate amnesty" for fighters would make it more difficult to reconstitute the M23, although he said there should be no impunity for rebels accused of "serious crimes". (Additional reporting by Aaron Maasho in Addis Ababa, Jenny Clover in Kigali and Pascal Fletcher in Pretoria; Writing by Edmund Blair and Richard Lough; Editing by James Macharia and Alistair Lyon)
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