Best way to do conditioned prices is use CBSubs Promotions and a negative promotion. This will let you condition the price based off a field value for example, a usergroup, or someones geographical location.
With that said there's no condition for payment type. So you can't condition against using PayPal for example. The best way to do that is have 2 copies of your plan and assign 1 to the PayPal gateway using the Owner ID parameter.
Q3 is it possible to integrate offline payments (cheques) from files/info sent periodically by our accountant?
Not sure what you mean, but users can attach files to their profile using a File fieldtype (built into CB 2.x).
Q4 is it possible to set a permanent automatic direct payment?
Nothing is permanent. Someone an cancel their subscription at any time, but recurring payments are doable depending on the gateway used.
Q5 and last. Is Joomaa 3 upgrade compulsory?
CB 2.x supports at minimum Joomla 2.5. This means so does CBSubs. However, Joomla 2.x is EOL (end-of-life) and you should strongly consider upgrading to Joomla 3.x as soon as possible.