Methane has a relatively short half-life, despite the bad press it has suffered over the last decade. It has typically degraded within 12 years (
source).
I think, in principal, your concern is a legitimate one but I don't think that it as, well, concerning as you might fear.
Simply burning wood will release all of the above, plus the carbon (mostly in the form of carbon dioxide) that would remain in the charcoal. Given that a stable wood-based fuel economy will need to regrow the same biomass of wood that it consumes, over a given period, at least as much carbon is then sequestered from the atmosphere to do so.
If we now examine the biochar situation, we know that some of the carbon remains after the burn and that this is locked up for a period of time in the soil. We also know that this improves the fertility and biodiversity of soil, allowing the soil to sequester further carbon, and providing additional benefits which, themselves, allow people nearby to decrease their emission (such as by growing food locally).
To further this, if the creation of the charcoal has secondary outputs - which it does, in the form of heat - and that these are used, some of the carbon (or other nasties) that is released has been offset. If you cook your dinner using the waste heat from your charcoal kiln, for example, you are saving the wood/gas/electricity that you would have otherwise used for that task. If you usually cook on wood, you can effectively deduct the emissions that quantity of wood would have produced from the negative outputs of your charcoal burn.
My recommendations would be that, if you're intending to produce biochar, you do so using wood obtained from a coppice or other system that promotes biomass (thus resequestering any carbon released) and that you try to utilise the "waste" heat as completely as possible.
What remains to be known is how much the addition of biochar to the soil increases that soils ability to further sequester carbon (without the need to add more biochar). It may be that, after a period of 2 year, adding 25kg of biochar to an area results in it sequestering a further 25kg (beyond the amount that it would have without the amendment). In this fictional scenario, you can feel secure in the knowledge that your actions have a net positive impact on the amount of carbon in the atmosphere. I'm afraid that I don't know of any data to back this up, however.
Further, there is the question of what would happen to a quantity of wood if left on the forest floor. Sure, it provides invaluable habitats for invertebrates (so does biochar, actually), but a large amount of it is digested and ends up as methane and carbon dioxide. Once again, I welcome actual figures for the amounts involved but my belief is that, in producing and digging in biochar, you are building carbon in the soil much faster than by waiting for leaf-litter and wood to compost over the same area (implying that more carbon is "lost" into the atmosphere by the natural processes).