Assuming my ship has only 1 anti-squadron armament (e.g. quasar):

Can I perform an anti-squadron attack against a squadron if line of sight is obstructed, but I have Kallus?

Even though I would remove my base anti-squadron armament, do I still add the Kallus die before the attack is cancelled (see pg. 2 of rrg under attacks)?

Kallus happens in the modify step so you need to be able to make the attack to begin with. Just like CF or Ackbar.

Adding a die occurs during the "modify and spend dice" step of the attack. Your attack fails because of step number 3, where you check if your attack battery still has dice.

In order, the steps are:

1. Check range, arc and line of sight
2. Assemble the appropriate dice in your battery armament (or anti-squadron armament when attacking enemy squadrons) as determined by range and arc. If you add or remove any dice from your battery armament, you do so now.
3. Check if you still have dice in your battery armament. If you have no dice, the attack fails and is automatically cancelled.
4. Roll any dice remaining in your battery armament. This is now your attack pool.
5. Modify dice step. Add, spend, or modify dice results in your attack pool in this step.
6. Spend Defense Tokens step. The defender may spend defense tokens now if they are able to do so. Some defense tokens may trigger immediately. Some defense tokens may trigger later. All defense tokens are "may" effects and do not have to be used to resolve their normal effect.
7. Resolve Critical Effects step. Anything that occurs during the critical effects step occurs now, including critical effects. If a critical effect modifies something that occurs later, it still must be declared first during this step (such as the Standard Critical Effect).
8. Damage step: total up the damage dealt by dice results (do not include damage caused by a critical effect). Anything that modifies the damage total or the type of damage done occurs during this step. Once the total amount of damage has been determined, apply it one point at a time to the defending ship hull zone or squadron.