To some money is no problem.
Stick with the score penelty, protect your race committee by enforcing compliance so you are not lookig for lazy owners or spoilt children at the end of racing. 

This will add a bit of extra workload for your volunteers, but if you want to use a progressive, non-scoring consequence approach.

1st miss: Quiet reminder after racing; incident noted for tracking.
2nd miss: Brief check-in with the PRO/Safety Officer before next launch to confirm expectations and fix any process issues.
3rd miss: Parent/guardian notified; sailor completes a short “back safely” plan (who they report to, where, and when) and reviews it with a coach or safety lead.

Further / willful non-compliance: Escalate as appropriate (e.g., require a meeting with event leadership, and only go to a hearing if necessary).

Many years ago, a group of 4 teenage Laser sailors failed to sign back in. The safety team stayed on the water for an hour until we found the sailors. As is was an evening event the safety team came ashore after dark, and were justifiably furious as the BBQ was no longer serving§
The RC protested the boats. I was chairing the PC. We gave the points penalty prescribed in the SIs. However, as the boys heaved a sigh of relief, I handed them all pen and paper and ordered them to write a letter of apology to the safety team leader.
One parent was close to accusing me of child abuse.
Years later I met one of the sailor at an event. He has a clear memory of the incident. He told me that writing the letter was a horrible penalty for teenage boys. However, he was clear that neither he nor any of the other sailors had ever failed to sign out/in ever since.
The club did the right thing - they fired up the BBQ for a late burger for both the crestfallen sailors and the safety team!

If safety is your real goal, then implement a safety based system, not a compliance-based one. My club requires that boats be kept on site and uses 'seagulls' to record every boat that launches and check them off as they return. Failure to be checked in may still be human error on the seagull's part, but you are not searching for a forgetful child who 'forgot'. Better yet, you are not failing to look for someone who is really missing but forgot to sign out in the morning.

Some events only give a 1 point penalty. I feel this relegates what is a serious safety issue to a minor annoyance. It also fails to show respect for the safety team. 
I should add that her in Ireland we take safety very seriously. This may in part due to the water temperature (7.5°C this weekend - 15° -16° in the summer)

I agree with Warren. 
We probably all agree that the OA has a responsibility to organise a safe event and that responsibility should remain with them, and they should not try to abdicate that responsibility onto the competitors with a bunch of rules and penalties. 
Another very simple way for the OA to check if competitors are missing at sea is to check the slipway for spare trollies after all visible sailors have come ashore. I've never found a sailor to "forget" to leave his trolley ashore when he launches, or simply drag his boat up a slipway after racing because he "forgot" he had a trolley to use. That simple check saved my daughter's life 35 years ago. If the safety vessels had to wait until a sign in time limit had expired, I doubt they would have found her in time.

We run single-handed offshore events so share the concerns with safety oversight but signing in and out isn't feasible and wouldn't address those.  The boats are required to use AIS so the RO can follow their track remotely.  If the whole fleet is becalmed at a headland with foul tide, that's sailing, but if one boat seems to be going in an odd direction or not moving well when the rest of the fleet is, we get worried.  We emphasise in the SIs the need to keep the RO informed if for any reason a boat's track could be concerning and reserve the right to refuse entry to future races.  In practice, I'm sure we'd adopt John's approach for the first offence (1st miss: Quiet reminder after racing; incident noted for tracking.)

"b) In the event of falling significantly behind other competitors (eg due to gear failure, fouling a net, or any other reason that a boat’s track may give rise to concern over the safety of the skipper), then every effort shall be made to get an appropriate message to the RO. If out of range for telephone contact, other methods should be used such as relaying a message via another competitor or contacting the coastguard using VHF.
It is imperative that unnecessary safety alerts are avoided and that yachts that are no longer competing can be excluded from any Search and Rescue operation. Failure to comply with the requirements of this section may lead to exclusion from future SORC racing.
c) The organisers may involve the authorities and emergency contact if they have concerns for the safety of any competitor. Competitors are encouraged to contact the RO if their progress may give cause for concern."
(Italicised text is in red font)

It should also be noted of course that the most likely source of assistance in offshore racing is another competitor, and we know that the competitors do watch out for each other.  It is not unusual for another competitor to call on VHF 'Are you ok?' and make sure they get a response.  When it is appopriate, boats have suspended racing to provide assistance or standby a boat that seems to have an issue (for which they obviously get redress).  

It's a rules penalty, no a performance penalty, not a safety penalty... See  RRS 1 though 4.  If you fail to enter properly you are disqualified, if you fail to conduct yourself in a sportsmanlike manner, disqualified.  Why would we hold sailor safety to a lessor standard?