Well like I said, I completely understand the reasoning behind the style of government implemented by the Tokugawa shogunate. I'm only saying that, particularly at the dawn of Japanese unification, it was not the only feasible way to bind the country together, establish peace, and preserve order. Religious toleration* does not invariably lead to chaos; allowing peasants to move about (provided they're still disarmed) may lead to fewer taxes in the short term, but allow for more efficient agriculture and growth in the longer term;** and even if policies like forbidding foreign travel are based on the desire to keep peace, they did isolate Japan (with all the problems that entailed) and can quite reasonably be seen as an overreaction (if an understandable one).
So yes, Oda can create a different solution to this, and in some ways his reforms, would have to resemble Hideyoshi's -- he's still going to want (and need) to conduct a census, collect taxes, and disarm the population, for example. But more aggressively conservative policies like tying the peasants to the land, restricting foreign travel, or clamping down on foreigners and Christianity -- policies like those boiled down to trading off future prospects for modest immediate gains or risk curbing. A less cautiously minded shogun may well have found these less appealing.
It would also help a huge deal if the ultimate solution to "excess" samurai got Japan something more than a disastrous war in Korea; better still if they can be used to establish successful *colonies* for Japan, which also helps with the above problems. (For example, Japan may feel less need for taking drastic measures against "idle" peasants if they have a convenient place to send them.)
*not the modern liberal idea of "freedom of conscience", but the more timeless idea that persecution is generally more trouble than it's worth
**and no, this analysis wasn't invented by Adam Smith