Personally, I feel that people read to much into the use of the gen-select device. It is not Tolwyn's weapon, it is, like the Dragon and the Flash-pak, a Confed R&D project. To me, the gen-select weapon is simply another weapon of mass destruction. If anything, it is far superior to the bio-weapons we know the Kilrathi, and presumably Confed, had been using throughout the war. It is a bio-weapon that can be programmed to attack specific targets, e.g. the Kilrathi, while leaving other targets untouched, e.g. Humans, native animals. Simply program it to attack the the Kilrathi have and we don't and it is a perfect weapon. It can be used freely on the battlefield without fear of affecting your own men, pump it through the ventilation systems of your ships as a protection against marine boarding parties (or to eliminate any pesky Pilgrims you might have on board ... oops, I've said too much).
Why it used on Telamon? Possibly quite simply because it is more readily available. By readily, I mean that Tolwyn can get his hands on it for use in a secret project. He can't easily walk into a Confed supply depot and ask say "can I have ten tonnes of bio-weapon please" without people asking awkward questions. On the other hand, an order from a high ranking officer to transfer some of Secret Project A from Top Secret Location 1 to Top Secret Location 2 would probably not attract questions at all (because people in top-secret R&D business soon learn that questioning orders leads to a brief appointment with strange people who do stuff like applying high voltages to peoples genitals while asking questions like "why were you asking questions about our top secret project").
To me, Tolwyn was always a true patriot and a strong leader. He did whatever was necessary, even if that involved the deaths of his own men. The ends justify the means.
What Tolwyn is facing at the beginning of WC4 is his, and probably a lot of other military officers, worst nightmare. Confed is in the middle of a post-war recession and, with no obvious enemies, the bean-counters in the goverment are severely cutting back military expenditure. The mighty Confed 'fleet' which defeated the Kilrathi is really just a collection of aging, battered vessels stretched across too many systems. The Versuvius class vessels designed to replace the older ones (like the Victory) are deemed too expensive. Soon the once-proud fleet will be a pile of rust and ANY enemy will have Confed at its mercy.
And there ARE enemies out there. The Kilrathi didn't just pack up and leave. While losses in the Kilrah system may have been costly, the fleet which had pushed Confed forces back nearly to Earth itself didn't just evaporate. Melek's decision to surrender is probably none too popular in certain corners of the empire. The Kilrathi may be more interested in internal squabbles then Confed, but should they unify under someone other then Melek ...
And the Border Worlds were always an uneasy ally in the Kilrathi War. I strongly doubt that the tensions growing between Confed and the Border Worlds were the work of Tolwyn or the Black Lance. All they did was blow on the embers.
For Tolwyn, the future is bleak. He has watched as the human race clawed its way back from the brink of oblivion (and they were soooo close to that), only to see them throwing it all away again. I imagine that he tried going through the 'proper' procedures. However some people would probably see it only as an effort of a faded memory trying to resurect past glory (Tolwyn's Behemoth failed, Paladins Temblar succeeded). Nobody is willing to listen. In desperation, he concocts a plan. Stir up some trouble with a known 'enemy', prove yourself right, and hope they listen. Some innocent people may die, but that cannot be helped. The ends justifies the means, and when the 'end' is the survival of the human race, this justifies some pretty strong 'means'.
Why pick on the Border Worlds? Because the Kilrathi are still very dangerous, even if most people don't realize this. If a conflict arises with the Kilrathi, Melek will lose what little support he does have and the entire Kilrathi war will start all over again.
Why does Tolwyn choose Blair? Why send him to Eisen's Lexington? Why Eisen for that matter? Because he needs Blair. Because people will listen to Blair, the hero of Kilrah and heart of the Tiger. Blair is part of the Plan. I would even go so far as to suggest that Tolwyn never even intends a full scale war with the Border Worlds. He doesn't need to. All he needs is for people to sit up and take notice, that there IS still a threat out there. So all he has to do stir up a bit of trouble, get Blair to report back to the council that yes, there is a problem. Once a threat is identified, they can divert some funds back into the military. Said trouble can be put down with a minimum of fuss, particularly with Blair there as a negotiator, then Blair can drift back into retirement and Tolwyn can say "I told you so, perhaps you'll listen to me in the future" and everybody will be happy. Unfortunately, things get a bit out of hand. Eisen gets wind that things are not as they seem and defects. Blair follows suit and everything goes downhill from there.
Why does Blair stick with the military? Because he knows that Tolwyn (and everybody else in the damn game
) was right - the price of freedom IS eternal vigilence. Blair knows that people will listen to him, when they didn't listen to Tolwyn. The Midway is Blairs compromise. It's not an all-out war-beast like the Versuvius, but it's better then the nothing they might have got without Tolwyn.
Funny really, that the person who gets what they wanted in the end is Tolwyn. The ends justify the means, even if the means is your own life.
Perhaps the quote that sums it up best comes from Blair at the end of WC4 : "What price freedom?"
Tolwyn's response : "Whatever it takes!"