On the other hand, this is a great opportunity to do some remodeling, like on that leaky wall!

I'm not sure I understand. Its entirely up to your players to figure out what they want to do. And though players are famous for doing the unexpected, there really is only a few broad approaches they can take....

(1)Assault. Either through the gate or over a wall. They go in swinging.

(2)Sneak in. Either a better way to do Assault (see 1). Or a black ops if your PCs have the right skills and temperament. Kill the ringleaders to inspire the rank and file to surrender.

(3)Diplomacy/Mind games

(4)Wait/Starve them out.

As a GM its your job its your job to have adventurous action ready regardless of what the PCs choose . Some options may make more sense than others. If the ronin's leader is not in the Keep then obviously you can sneak in and kill him.

(1b)Assault has the most permutations...but it's also the most straightforward. How many opponents do you make the PCs fight? And at what locations does it happen? IMO its generally not a good idea for low level PCs to be able to walk over a garrison behind walls. One it's not realistic for their skill level. Two, if they can do it here they'll want to do it in other places. Three why aren't other low level samurai doing the same thing elsewhere?

IMO Storming the gate during the day in a full assault probably should result in high casualties (not necessarily the players) that cause their daimyo manpower shortages down the road. There should be bigger advantages for successfully sneaking in at night. Or pulling off a Trojan Horse/Secret Tunnel maneuver.

(2b) Could be appropriate. Someone is in charge of the Keep. And they probably have a few "helpers" as their deputies. Even if the real leader is gone. If the PCs want to sneaky-sneaky get these people you need to know if they can slip in (walls or tunnel), what guards (if any) they need to sneak past, and how long it takes the camp to respond to the sounds of combat (sneaky PCs or the right spells or Kihos might make it hard for an alarm to be raised).

(3b) Who do the PCs actually parlay with? That guy (or gal) is an NPC. What terms are acceptable to this ronin? the ronin in general? the ronin leadership? to the PCs Lord? There may be daylight there for the PCs to exploit. Ultimately this is up to you to set TNs and preconditions for success (We'll surender, but only if you kill Psyco Bob first...he terrifies us!). A group of Ronin might have issues with the current leadership and be "persuadable" to turn a blind eye to PCs "changing leadership" ... see 2. In the Alternative, maybe the PCs can recruit Ronin into their new clan (perhaps they need to pass certain tests...like eliminate those who resist the change). Or maybe the PCs find the people in town who are the ronin's hangers on, and get them to implement a plot. Like they have to lie and tell the ronin that they have to "rescue" their leader who "has been captured and will be hung at dawn!" Or send over spiked booze... Who are these people. How do the PCs gain leverage over them?

(4b) Not very exciting but logical and historically effective. What additional civic trouble can you create for the PCs while they linger for a week or two to starve them out? A skirmish from attackers in the Keep? A daimyo who wants the PCs to storm the walls? A procession of Priests/Monks who demand to access the Shrine. A riot in another part of the city? The Kami by the Keep become unhappy because the Drunken ronin have disturbed it?