Not a priority problem for the survivors
Let's be clear, this is a straightforward apocalypse scenario. If a society loses 5-10% of its population unexpectedly then civilisation will collapse. If it suddenly loses over 98% of its population then there's nothing left - the survivors will be desperately looting all stockpiles for enough essential supplies to survive the next few days. Fortunately, this is just one country, so the populace have other countries to flee to and with less than 2% of the original population they should easily be able to find enough food to get there. Dealing with the bodies will be a problem for the countries that decide to move in and occupy the vacant land.
In the unlikely event that this country is so isolated that there is nowhere to go, the survivors will need to pick a few small towns and try to secure them - towns that are close to power plants and agricultural areas are preferred. Initially the priority will be to clear bodies out of the locations with critical infrastructure - power plants, communications nodes, fuel depots, hospitals and so on - so that these areas can be used. Whatever is done will be the absolute minimum effort to get things functioning again - there will not be the manpower available to undertake even basic graves registration procedures, most likely is to pick a flammable, non-critical building with a good firebreak around it and dump them in there, then ignite it on a day where a light wind is blowing away from the buildings occupied by the living.
Once the immediate needs of the survivors are taken care of - enough housing available, clean water, sewerage, power and minimal communications restored, remaining food and medical stores consolidated - the only viable way for the country to survive in the short term will be to cannibalise the wealth (not the bodies) of the previous population. I would guess that while roughly half the able-bodied population maintain infrastructure (and hopefully start growing food for when the canned supplies run out) that the rest will be sent out in parties to secure what wealth remains. This will include:
- Stripping unused vehicles for parts to keep the required 2% running.
- Scavenging fuel and lubricants from all vehicles, household garages and businesses.
- "Government approved" looting of valuables for trading with other countries for key supplies.
- Surveying locations of stockpiles of resources - everything from bricks and timber to plumbing supplies to stationery to diagnostic imaging devices. In particular, find as much plastic sheeting/garbage bags and disinfectant as possible.
As areas are surveyed, looted and cleared the bodies will need to be dealt with. Without extraordinarily cold weather conditions, by this time all bodies will have decayed and suffered significant consumption by insects and rodents, as well as possibly larger animals. As previously, the priority will be to expend minimal effort, resources and time dealing with the bodies. There are good reasons that burial and cremation have been the most common methods of disposing of bodies in history. Incineration requires a lot of fuel per body, so it would be more sensible to use bulldozers and backhoes to dig trenches for mass graves, especially as there is plenty of land to go around with 98% of the population gone.
This would be extraordinarily traumatic work. A long time ago I spoke with a soldier from INTERFET who had to recover the bodies of civilians, including children, who were killed and dumped down a well in East Timor. Without going into details, dealing with badly decomposed bodies that come apart when you try to move them, day after day, will psychologically scar the scavenging parties. It would become much easier both physically and psychologically after more time when the bodies are reduced to being mostly skeletons with a minimum of mummified flesh remaining.
While there theoretically are other ways of dealing with the bodies - such as turning them into fertiliser - I cannot envisage such alternatives being considered given the psychological aspects.
In summary - short term, put bodies in an expendable, inflammable building and set fire to it when the wind conditions are as good as they are going to get. Long term, dig trenches for mass graves as it will require less resources.