Sure.  Create a aws_config_stack, which you deploy once per account/region pair.
In the constructor, get the environment's rule names from DynamoDB with a get_item SDK call. The boto3 command gets called at synth-time, which is keeping with CDK best practices.
Define the rules in whatever files you want.  Wrap each rule in a function that accepts a scope and returns the rule:
# make_access_keys_rotated_rule.py
# One function per ManagedRule.  Add to the rule dictionary.  Called by `make_rule`
def make_access_keys_rotated_rule(scope: Construct) -> config.ManagedRule:
    return config.ManagedRule(scope, "AccessKeysRotated",
        identifier=config.ManagedRuleIdentifiers.ACCESS_KEYS_ROTATED,
        input_parameters={
            "max_access_key_age": 60
        },
        maximum_execution_frequency=config.MaximumExecutionFrequency.TWELVE_HOURS
    )
Add each rule function to a dictionary, where the keys are the rule name.  Perhaps add the dictionary lookup logic to a method in your aws_config_stack subclass.  A make_rule method looks up the rule-making function by name and executes it, adding a single rule to the stack.
# aws_config_stack.py method
# Look up and execute a ManagedRule function by rule name.  Called in the constructor.
def make_rule(self: Construct, rule_name: str) -> config.ManagedRule:
    rule_dict = {
        "AccessKeysRotated": make_access_keys_rotated_rule
    }
    return rule_dict[rule_name](self)
Finally, in the stack constructor, call make_rule for every name in the rule-name list from DynamoDB.
# aws_config_stack.py constructor
rules: list[config.ManagedRule] = [self.make_rule(r) for r in rule_names_from_dynamo]
After synth, a cdk diff should reveal rules being added and deleted from the stack to match the list from DynamoDB.
P.S. Optionally add the Delivery Channel (CfnDeliveryChannel + Bucket) resources and Configuration Recorder (CfnConfigurationRecorder + Role) resources to the same stack to have the CDK fully manage the AWS Config resources.