Initialization of the RFM69 essentially just boils down to setting about a dozen values in its registers. While it isn't the same, here is my own custom radio initialization code that is quite simple to follow. Change_OP_Mode is just a #define for me. Perhaps your SPI bus is on rather than being shut down?
#define CHANGE_OP_MODE(mode) writeReg(REG_OPMODE, mode)
static inline void RadioInit(void) {
SPI_INIT();
CHANGE_OP_MODE(SLEEP_MODE); // Put the radio to sleep ASAP to save power
writeReg( REG_BITRATEMSB, RF_BITRATEMSB_300000 ); // 0x03
writeReg( REG_BITRATELSB, RF_BITRATELSB_300000 ); // 0x04
writeReg( REG_FDEVMSB, RF_FDEVMSB_300000 ); // 0x05
writeReg( REG_FDEVLSB, RF_FDEVLSB_300000 ); // 0x06
writeReg( REG_RXBW, RF_RXBW_DCCFREQ_111 | RF_RXBW_MANT_16 | RF_RXBW_EXP_0 ); // 0x19
writeReg( REG_RSSITHRESH, 220 ); // 0x29
writeReg( REG_SYNCCONFIG, RF_SYNC_ON | RF_SYNC_FIFOFILL_AUTO | RF_SYNC_SIZE_2 | RF_SYNC_TOL_0 ); // 0x2E - 2 sync bytes
writeReg( REG_SYNCVALUE1, 0x3D ); // 0x2F
writeReg( REG_SYNCVALUE2, NETWORKID ); // 0x30
//writeReg( 0x31, 0xAA ); // 0x31
writeReg( REG_PACKETCONFIG1, RF_PACKET1_FORMAT_VARIABLE | RF_PACKET1_DCFREE_OFF | RF_PACKET1_CRC_OFF | RF_PACKET1_CRCAUTOCLEAR_OFF | RF_PACKET1_ADRSFILTERING_OFF ); // 0x37 // 0x37
//writeReg( REG_AUTOMODES, AUTO_TRANSMITTER ); // 0x3B - Put the radio in automatic mode
writeReg( REG_PACKETCONFIG2, RF_PACKET2_RXRESTARTDELAY_2BITS | RF_PACKET2_AUTORXRESTART_ON | RF_PACKET2_AES_ON ); // 0x3D
writeReg( 0x6F, 0x30 );
SET_POWER_LEVEL(0);
}
De-init would be setting these registers back to their power-on default values which can be obtained from the datasheet. As Felix said, changing their values back should not effect power draw but experimentation is easy so go for it.