Many of the former Boereleiers (Boer leaders) were the only people with the credibility to potentially run the Transvaal and Orange River Colonies when they got self-government (responsible government) back in 1906 and 1907 respectively. This recognition came from Lord Selbourne's ministry in London, which had to make these kinds of calls pursuant to the terms of peace in 1902, and represented an admission that Milnerization--the attempt to 'flood out' via immigration or otherwise discredit the old Republican leadership and sideline emerging ideas of a single Afrikaner culture--had ultimately failed. (Torrance's The Strange Death of the Liberal Empire: Lord Selbourne in South Africa has a fair bit on this conversion to an Afrikaner nationalist regime from the eyes of London.)

At the same time, it wasn't clear that the British could have--or should have tried to--block Boer generals from standing for office. The terms of the Treaty of Vereeniging were very clear that a general amnesty was part of it, for all who laid down arms, and swore an oath of allegiance to the Crown (clauses 5 and 3 respectively). The generals agreed to those terms and carried them out; some people who could not or would not in fact departed, like the forebears of the Boer towns in northern Argentina, and some who went to South-West Africa (Namibia) or the Portuguese territories. If the British had disqualified former combatants or officials of the Republics, they'd have been without most of a civil service, and utterly lacking credibility. The end of the war for Britain was about restoring honor and, in no small measure, assuring a combined white supremacy. Botha, the popular field general, had been willing to treat with the British and negotiate forcefully, and Smuts, who was in fact educated in the UK (Cambridge) and a member of the Middle Temple, was a Capetonian law scholar originally [edit: before taking up the post of Attorney General in the South African Republic / Transvaal at a very young age]. By 1906 it was obvious that the Afrikaner parties--the Afrikaner Bond (Cape), Het Volk (Transvaal), and Oranje Unie (ORC)--could be either partners or opponents, but either way, they were the most powerfully united political forces in those territories, and would eventually merge in some way (which they did as the SA Party). Disqualifying popular wartime leaders who had remained undefeated in the field would have made them implacable foes.

Even making them into partners didn't guarantee loyalty to Britain or its proffered interests; witness the many anti-British lives of Manie Maritz (of the 1914 Rebellion) for that stunning story of repeated forgiveness in the Union, or the later cases of the Gesuiwerde Nasionale Party under DF Malan that turned into the core of apartheid proper. But then, those seemed like minorities, and they never really threatened British capital and investments in the first place. Maritz, De Wet, et al. were doomed in 1914; Malan was smart enough to try to reconcile the English-speakers, at least until he was pushed from office in the early years of apartheid.