What I gather from the years of reading manga (and one discussion with a European, who worked in Japan for 5 years), the relation between a company and an employee is much closer there. It is assumed a company is almost like a family and an employee's behaviour represents the company at all times. So for example, the company is often a guarantor when renting a flat, but on the other all the troublesome actions by the employee can cause him to be fired. Also the reputation is very important there, and a company that is surrounded by rumours and scandals, wouldn't be treated as a serious business partner.
It also seems that an affair itself isn't treated as something as morally wrong, as in Europe/US (see that there's even a special procedure for financial compensation). It is even expected from men [sic!] at some social level to have a mistress. If I understand correctly, if one of his colleagues saw Junpei in Gifu with some random woman, he'd get a pat on the back and perhaps a little warning to be more subtle about it. Where he failed was, that Rina was in fact a company employee and that he got caught. Office affairs are a huge no-no and legal actions provide a big blow to a company's reputation. With that in mind, if Junpei had told the real reason why he needed a transfer, he would have been let go/forced to quit anyway.
Now everyone is angry at him not only because he lied to them (I assume it's universal and people just don't like being lied to), but also because he wanted to skip the consequences of his actions, which is also a behaviour very frowned upon in Japan.
If someone has better understanding, please correct me.