1. Let's first address Sage Mode not being necessary against Obito. First off, Minato did not know it was Obito. He thought it was Madara. Based on his deductions that gave him the conclusion of Madara, and his dialogue concerning Madara, such as that he'd bring trouble for the whole world, it means Minato knows that Madara is extremely powerful and dangerous. It means Minato was taking Obito with the utmost seriousness. This is an individual that was capable of sneaking into Konoha, and taming the Kyubi without being a Jinchuriki, the later is something even Minato could not accomplish. He was able to sneak past Minato to get into Kushina's birthing area. There is no good reason as to why Minato would not deal with him permanently. He killed that random fodder back when Kakashi first used Chidori, why would he attack who he thinks is Madara with intent to kill? There is no good reason as to why Minato did not use it against Obito, other than the fact that Kishi only recently decided that Minato would have Sage Mode. That in itself makes it an asspull.
2. KM/BM being stronger does not matter. What matters is the power that is more useful. When locating and removing the chakra rods from the Bijuu, Naruto used Sage Mode because he knew it was more useful in that situation, even though KM was stronger. If a complete shitbrain like Naruto was able to figure that out, and make such a good judgement, why wouldn't Minato? Minato is very intelligent, so do you really think it makes sense that he would stay in KM and not use SM at any point? Think about it, Naruto is already using BM and SM. If SM is Juubito's weakness, wouldn't it make more sense and be more efficient to have two SM users and one BM user, rather than one SM user and two BM users? Wouldn't it make sense for Minato to figure that out?