Given the complicated nature of the question(s), I'm going to break it up and answer it in pieces, not necessarily in the same order as it was presented.
Do you continue to use penalties for extended sympathetic casting, identically to instant sympathetic casting?
Yes. Sympathy isn't a spell factor like Area and Duration. Spell factors are optional ways for the caster to customize the effects of the spell, while sympathy is a penalty that makes it more difficult to make the magic happen due to a lack of connection with the target. It's a barrier to making the magic happen at all, as opposed to a nice extra that increases the difficulty.
This is doubly true when you remember the rule for extended actions in the Core Rulebook that states that the number of attempts on extended actions you can take is limited by your dice pool.
The World of Darkness states the limitation as equal to the character's Attribute + Skill total (p. 128).
...does this mean that sympathetic "attacks" would almost certainly require disciple and lower level mages to resort to cabal level group rituals...
Note that actual attack spells (ones that directly affect the Pattern of the target) require an additional Arcanum dot. So you can do bashing damage at Adept level, or lethal at Master level. Indirect attacks don't have this problem, which gives PCs an incentive to be creative. Indirect attacks also don't rely on Potency to determine how much damage they do (using Matter to drop a wall on someone through a scrying window is going to be treated the same way that any wall falling over would be), so if you can score a success or three, you're golden.
Sympathetic attack spells are generally bad ideas for other reasons, such as how they allow the target to counter-attack (even without possessing Space) and are always vulgar, no matter what. The lower average Potency is also going to make your attack very vulnerable to being counterspelled.
what effects does it have on extended attack magic (Which is specifically mentioned in Tome of the Mysteries as often being Sympathetic, despite what seems like possibly tremendous penalties after all the bonuses and penalties are combined).
Extended attack magic (almost always) has to be sympathetic, because no target is going to sit still for nine hours while you summon their death. The effect that the sympathy and ritual casting time rules have is to heavily discourage extended, sympathetic attacks. You aren't supposed to be able to instakill anybody you want from the privacy of your sanctum. At least, not unless you're a Master with high Gnosis.
The book Armory has official rules for stun batons, a paragraph under Stun guns, on p. 36.
The entry describes how stun guns work (short: the electricity doesn't cause damage, it knocks the target unconscious for a specific number of rounds), and
A baton version of this weapon [of the stun gun] exists. The baton can
be used as a club to cause damage (+1 modifier to attack, does bashing
damage only) or it can be used to deliver a charge from its tip. The
baton cannot be used to do both.
Armory p.93 has an entry on Ranged Stun Guns, though, in whose description you'll find that firing the probes of a ranged stun gun causes a level of bashing damage besides (that is, simultaneously) having the effects of a standard stun gun.
If your weapon is a standard issue stun baton, use the rules presented in Armory. If it's something specific, an experimental piece that you and your GM cooked up in and for the story, use it as your GM says, because, as you've said, he's the GM. :)
If you're interested in my subjective opinion, I'd say a mad scientist's super-advanced stun baton would cause bashing damage along with the stun effect described in Armory.
Best Answer
On extended actions, you usually get results on the 5th, 10th, 15th etc. accumulated success'. so by definition the amount of success' rolled on extended action rolls, have a direct impact on the result, for instant actions a single success is mostly enough to achieve desired result. With that said, if the ST wrote down what would happen on 5, 10 and 15th success and you achieve 19, you'll just get the results of 5,10 and 15, but if you achieve 20, you will get a more precise result than you or ST anticipated. hence an exceptional success. 15 success might be the breaking point where the initiators assume the action can't be perfected more and stop the extended action. in other words they achieve what they hoped for and more effort would seem meaningless.
for example a cultist leader trying to convert people into his cult might initiate an extended roll on recruitment (let's say manipulation + persuasion, dice pool: 6) he rolls each day and once he recruits 2 people he intends to count this a success and stop. the ST decides that each people he wishes to recruit, needs 5 success. so for 2 people he'd need 10 successes. initiator rolls and after 4th roll he achieves 9 success. next day he rolls again and this time he gets 6 success. this is an exceptional success. so not only achieves the cult leader his goal of recruiting 2 people into his cult, he might also found the perfect candidates, who would devote themselves to the cult completely. which wasn't the initial goal but enhances the result in favor of the initiator.